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\title{NucleoMiner2 Documentation}
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\date{\today}
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\author{Florent CHUFFART, Jean-Baptiste VEYRIERAS, Gael YVERT}
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\newcommand{\sphinxlogo}{}
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\makeindex |
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\begin{document}
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\maketitle |
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\tableofcontents |
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\textbf{}\label{index::doc}
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\section{Inferring Nucleosome Position and Extracting Read Counts}
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\label{tuto:inferring-nucleosome-position-and-extracting-read-counts}
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The second part of the tutorial uses R (\url{http://http://www.r-project.org}{http://http://www.r-project.org}).
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It consists in 5 main steps: |
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\begin{itemize}
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\item {}
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Seting Up Configuration |
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\item {}
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Computing CURs |
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\item {}
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Extracting Nucleosome Maps from TemplateFilter Outputs |
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\item {}
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Building Count Tables from TemplateFilter Inputs |
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\item {}
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Analysing Count Tables using DESeq |
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\end{itemize}
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\subsection{Seting Up Configuration}
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This first step is in charge of: |
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\begin{itemize}
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\item {}
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launching libraries used in the scripts |
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\item {}
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launching configuration (design, strain, marker...) |
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{\footnotesize
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<<echo=TRUE, results=hide>>= |
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library(nucleominer) |
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@ |
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<<echo=TRUE, results=verbatim>>= |
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package.version("nucleominer")
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library(rjson) |
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json_conf_file = "nucleominer_config.json" |
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config = fromJSON(paste(readLines(json_conf_file), collapse="")) |
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all_samples = read.csv(config$CSV_SAMPLE_FILE, sep=";", head=TRUE, stringsAsFactors=FALSE) |
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head(all_samples) |
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markers = unique(all_samples$marker) |
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print(markers) |
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strains = unique(all_samples$strain) |
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print(strains) |
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combis = combn(strains, 2, simplify=FALSE) |
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print(combis) |
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@ |
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} |
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\subsection{Computing CURs}
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This second step is in charge of computing and caching Common Uinterrupted Regions (CURs). Caching means storing the information in the computer's memory. |
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\end{itemize}
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Note that you can customize the function “translate”. This function allows you to use the alignments between genomes when performing various tasks. |
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\begin{itemize}
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\item {}
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You may want to analyze data of a single strain (e.g. treatment/control, or only few mutations). In this case, the genome is identical across all samples and you do not need to define particular CURs (CURs are chromosomes). Simply use the default translate function which is neutral. |
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\item {}
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If you are analyzing data from two or more strains (as NucleoMiner2 was designed for), then you need to translate coordinates of one genome into the coordinates of another one. You must do this by aligning the two genomes, which will produce a .c2c file (see Appendice ``Generate .c2c Files''). thenuse it to produce the list of regions and customise “translate”. |
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\end{itemize}
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In our tutorial, we are in the second case and to perform all these steps run the following command line in your R console: |
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{\footnotesize
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<<echo=TRUE, results=hide>>= |
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curs = compute_curs(diff_allowed=30, min_cur_width=4000, combis, config) |
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@ |
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<<echo=TRUE, results=verbatim>>= |
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head(curs) |
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# Reduce first CUR length to accelerate demo, TODO: remove it before submission. |
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curs [1,3] = curs[1,3] - 110000 |
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curs [1,5] = curs[1,5] - 110000 |
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@ |
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} |
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\subsection{Extracting Nucleosome Maps from TemplateFilter Outputs}
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This third step is in charge of extracting Maps for well-positioned and sensitive nucleosomes. First of all, this script computes intra and inter-strain matches of nucleosome maps for each CUR. This step can be executed in parallel on many cores using the BoT library. Next, it collects results and produces maps of well-positioned nucleosomes, sensitive nucleosomes and Unaligned Nucleosomal Regions . |
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The map of well-positioned nucleosomes for BY is collected in the result directory and is called \emph{BY\_wp.tab}. It is composed of following columns:
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\begin{itemize}
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\item {}
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chr, the number of the chromosome |
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\item {}
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lower\_bound, the lower bound of the nucleosome |
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\item {}
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upper\_bound, the upper bound of the nucleosome |
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\item {}
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cur\_index, index of the CUR |
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\item {}
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index\_nuc, the index of the nucleosome in the CUR |
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\item {}
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wp, 1 if it is a well positioned nucleosome, 0 otherwise |
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\item {}
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nb\_reads, the number of reads that support this nucleosome |
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\item {}
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nb\_nucs, the number of TemplateFilter nucleosome across replicates (= the number of replicates in which it is a well-positioned nucleosome) |
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\item {}
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llr\_1, for a well-positioned nucleosome, it is the LLR1 (log-likelihood ratio) between the first and the second TemplateFilter nucleosome on the chain. |
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\item {}
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llr\_2, for a well-positioned nucleosome, it is the LLR1 between the second and the third TemplateFilter nucleosome on the chain. |
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\item {}
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wp\_llr, for a well-positioned nucleosome, it is the LLR2 that compares consistency of the positioning over all TemplateFilter nucleosomes. |
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\item {}
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wp\_pval, for a well-positioned nucleosome, it is the p-value chi square test obtained from LLR2 (\emph{1-pchisq(2.LLR2, df=4)})
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\item {}
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dyad\_shift, for a well-positioned nucleosome, it is the shift between the two extreme TemplateFilter nucleosome dyad positions. |
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\end{itemize}
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The sensitive map for BY is collected in the result directory and is called \emph{BY\_fuzzy.tab}. It is composed of following columns:
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\begin{itemize}
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\item {}
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chr, the number of the chromosome |
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\item {}
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lower\_bound, the lower bound of the nucleosome |
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\item {}
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upper\_bound, the upper bound of the nucleosome |
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\item {}
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cur\_index, index of the CUR |
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\end{itemize}
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The map of common well-positioned nucleosomes aligned between the BY and RM strains is collected in the result directory and is called \emph{BY\_RM\_common\_wp.tab}. It is composed of following columns:
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\begin{itemize}
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\item {}
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cur\_index, the index of the CUR |
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\item {}
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index\_nuc\_BY, the index of the BY nucleosome in the CUR |
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\item {}
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index\_nuc\_RM, the index of the RM nucleosome in the CUR |
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\item {}
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llr\_score, , the LLR3 score that estimates conservation between the positions in BY and RM |
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\item {}
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common\_wp\_pval, the p-value chi square test obtained from LLR3 (\emph{1-pchisq(2.LLR3, df=2)})
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\item {}
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diff, the dyads shift between the positions in the two strains (in bp) |
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\end{itemize}
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The common UNR map for BY and RM strains is collected in the result directory and is called \emph{BY\_RM\_common\_unr.tab}. It is composed of the following columns:
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\begin{itemize}
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\item {}
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cur\_index, the index of the CUR |
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\item {}
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index\_nuc\_BY, the index of the BY nucleosome in the CUR |
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\item {}
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index\_nuc\_RM,the index of the RM nucleosome in the CUR |
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\end{itemize}
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To execute this script, run the following command in your R console: |
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{\footnotesize
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<<echo=TRUE, results=hide>>= |
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build_maps(strains, combis, all_samples, curs, config) |
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@ |
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<<echo=TRUE, results=verbatim>>= |
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BY_wp = read.table("outputs/BY_wp.tab", header=TRUE)
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head(BY_wp) |
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RM_wp = read.table("outputs/RM_wp.tab", header=TRUE)
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head(RM_wp) |
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BY_RM_common_wp = read.table("outputs/BY_RM_common_wp.tab", header=TRUE)
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head(BY_RM_common_wp) |
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@ |
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} |
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\subsection{Building Count Tables from TemplateFilter Inputs
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} |
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\label{tuto:the-script-count-reads-r}
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To associate a number of observations (read) to each nucleosome we run the script \emph{count\_reads.R}. It produces the files \emph{BY\_RM\_H3K14ac\_wp\_and\_nbreads.tab}, \emph{BY\_RM\_H3K14ac\_unr\_and\_nbreads.tab} \emph{BY\_RM\_Mnase\_Seq\_wp\_and\_nbreads.tab} and \emph{BY\_RM\_Mnase\_Seq\_unr\_and\_nbreads.tab}
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for H3K14ac common well-positioned nucleosomes, H3K14ac UNRs, Mnase common well-positioned nucleosomes and Mnase UNRs respectively. |
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For example, the file \emph{BY\_RM\_H3K14ac\_unr\_and\_nbreads.tab} contains counted reads for well-positioned nucleosomes with the experimental condition ChIP H3K14ac. It is composed of the following columns:
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\begin{itemize}
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\item {}
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chr\_BY, the number of the chromosome for BY |
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\item {}
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lower\_bound\_BY, the lower bound of the nucleosome for BY |
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\item {}
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upper\_bound\_BY, the upper bound of the nucleosome for BY |
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\item {}
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index\_nuc\_BY, the index of the BY nucleosome in the CUR for BY |
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\item {}
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chr\_RM, the number of the chromosome for RM |
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\item {}
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lower\_bound\_RM, the lower bound of the nucleosome for RM |
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\item {}
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upper\_bound\_RM, the upper bound of the nucleosome for RM |
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\item {}
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index\_nuc\_RM,the index of the RM nucleosome in the CUR for RM |
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\item {}
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cur\_index, index of the CUR |
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\item {}
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BY\_H3K14ac\_36, the number of reads for the current nucleosome for the sample 36 |
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\item {}
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BY\_H3K14ac\_37, \#reads for sample 37 |
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\item {}
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BY\_H3K14ac\_53, \#reads for sample 53 |
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\item {}
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RM\_H3K14ac\_38, \#reads for sample 38 |
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\item {}
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RM\_H3K14ac\_39, \#reads for sample 39 |
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\end{itemize}
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To execute this script, run the following command in your R console: |
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{\footnotesize
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<<echo=TRUE, results=hide>>= |
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for (form in c("wp", "unr")) {
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for (marker in markers) {
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build_count_table(marker, combis[[1]], form, curs, all_samples, config) |
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} |
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} |
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@ |
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<<echo=TRUE, results=verbatim>>= |
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a_count_table = read.table("outputs/BY_RM_Mnase_Seq_wp_and_nbreads.tab", header=TRUE)
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head(a_count_table) |
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@ |
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} |
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\subsection{Analysing Count Tables using DESeq}
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Finally, the script \emph{launch\_deseq.R} perform statistical analysis on each nucleosome using \emph{DESeq}. It produces files:
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\begin{itemize}
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\item {}
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results/current/BY\_RM\_H3K14ac\_wp\_snep.tab |
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\item {}
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results/current/BY\_RM\_H3K14ac\_unr\_snep.tab |
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\item {}
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results/current/BY\_RM\_H3K14ac\_wpunr\_snep.tab |
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\end{itemize}
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These files are organised with the following columns (see file \emph{BY\_RM\_H3K14ac\_wp\_snep.tab} for an example):
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\begin{itemize}
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\item {}
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chr\_BY, the number of the chromosome for BY |
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\item {}
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lower\_bound\_BY, the lower bound of the nucleosome for BY |
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\item {}
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upper\_bound\_BY, the upper bound of the nucleosome for BY |
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\item {}
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index\_nuc\_BY, the index of the BY nucleosome in the CUR for BY |
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\item {}
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chr\_RM, the number of the chromosome for RM |
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\item {}
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lower\_bound\_RM, the lower bound of the nucleosome for RM |
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\item {}
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upper\_bound\_RM, the upper bound of the nucleosome for RM |
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\item {}
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index\_nuc\_RM,the index of the RM nucleosome in the CUR for RM |
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\item {}
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cur\_index, index of the CUR |
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\item {}
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form |
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\item {}
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BY\_Mnase\_Seq\_1, the number of reads for the current nucleosome for the sample 1 |
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\end{itemize}
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Next columns concern indicators for each sample: |
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\begin{itemize}
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\item {}
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BY\_Mnase\_Seq\_2, \#reads for sample 2 |
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\item {}
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BY\_Mnase\_Seq\_3, \#reads for sample 3 |
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\item {}
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RM\_Mnase\_Seq\_4, \#reads for sample 4 |
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\item {}
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RM\_Mnase\_Seq\_5, \#reads for sample 5 |
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\item {}
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RM\_Mnase\_Seq\_6, \#reads for sample 6 |
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\item {}
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BY\_H3K14ac\_36, \#reads for sample 36 |
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\item {}
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BY\_H3K14ac\_37, \#reads for sample 37 |
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\item {}
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BY\_H3K14ac\_53, \#reads for sample 53 |
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\item {}
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RM\_H3K14ac\_38, \#reads for sample 38 |
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\item {}
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RM\_H3K14ac\_39, \#reads for sample 39 |
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\end{itemize}
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The 7 last columns concern DESeq analysis: |
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\begin{itemize}
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\item {}
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manip{[}a\_manip{]} strain{[}a\_strain{]} manip{[}a\_strain{]}:strain{[}a\_strain{]}, the manip (marker) effect, the strain effect and the snep effect. These are the coefficients of the fitted generalized linear model.
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\item {}
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pvalsGLM, the pvalue resulting from the comparison of the GLM model considering the interaction term \emph{marker:strain} to the GLM model that does not consider it. This is the statsitcial significance of the interaction term and therefore the statistical significance of the SNEP.
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\item {}
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|
| 409 |
snep\_index, a boolean set to TRUE if the pvalueGLM value is under the threshold computed with FDR function with a rate set to 0.0001. |
|
| 410 |
|
|
| 411 |
\item {}
|
|
| 412 |
mnase\_l2fc, this is the coefficients of the fitted generalized linear model based on MNASE samples only. |
|
| 413 |
|
|
| 414 |
\item {}
|
|
| 415 |
mnase\_l2fc\_pval, the pvalue resulting from the analysis of the simple model based on MNASE samples only. This is the statsitcial significance of the \emph{strain} term and therefore the statistical significance of the strain effect.
|
|
| 416 |
|
|
| 417 |
\end{itemize}
|
|
| 418 |
|
|
| 419 |
To execute this script, run the following command in your R console: |
|
| 420 |
|
|
| 421 |
|
|
| 422 |
{\footnotesize
|
|
| 423 |
<<echo=TRUE, results=hide>>= |
|
| 424 |
for (form in c("wp", "unr", "wpunr")) {
|
|
| 425 |
sneps = analyse_count_table(markers[2], combis[[1]], form, all_samples, config=config) |
|
| 426 |
} |
|
| 427 |
@ |
|
| 428 |
<<echo=TRUE, results=verbatim>>= |
|
| 429 |
a_sneps_table = read.table("outputs/BY_RM_H3K14ac_wp_snep.tab", header=TRUE)
|
|
| 430 |
head(a_sneps_table) |
|
| 431 |
|
|
| 432 |
@ |
|
| 433 |
} |
|
| 434 |
|
|
| 435 |
Here are the number of computed SNEPs for each forms. |
|
| 436 |
|
|
| 437 |
|
|
| 438 |
|
|
| 439 |
|
|
| 440 |
\end{document}
|
|
| b/doc/R_tutorial/data/BY_RM_chr1.c2c | ||
|---|---|---|
| 1 |
chrI 27017 27632 c + - supercontig_1.17 -1 192140 191525 |
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chrI 27644 27765 c + - supercontig_1.17 -1 191513 191392 |
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chrI 29284 29284 c + d supercontig_1.17 -1 189868 189866 |
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chrI 29285 29429 c + - supercontig_1.17 -1 189865 189721 |
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chrI 29430 29434 c + i supercontig_1.17 -1 189721 189721 |
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chrI 29435 29462 c + - supercontig_1.17 -1 189720 189693 |
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chrI 29463 29463 c + i supercontig_1.17 -1 189693 189693 |
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chrI 29464 29535 c + - supercontig_1.17 -1 189692 189621 |
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| 32 |
chrI 29535 29535 c + d supercontig_1.17 -1 189620 189620 |
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chrI 29536 29553 c + - supercontig_1.17 -1 189619 189602 |
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| 34 |
chrI 29554 29554 c + i supercontig_1.17 -1 189602 189602 |
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| 35 |
chrI 29555 29606 c + - supercontig_1.17 -1 189601 189550 |
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chrI 29606 29606 c + d supercontig_1.17 -1 189549 189549 |
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chrI 29607 29753 c + - supercontig_1.17 -1 189548 189402 |
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| 38 |
chrI 29753 29753 c + d supercontig_1.17 -1 189401 189401 |
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| 39 |
chrI 29754 29767 c + - supercontig_1.17 -1 189400 189387 |
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chrI 29768 29768 c + i supercontig_1.17 -1 189387 189387 |
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chrI 29847 29847 c + d supercontig_1.17 -1 189308 189307 |
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chrI 29848 29873 c + - supercontig_1.17 -1 189306 189281 |
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chrI 29873 29873 c + d supercontig_1.17 -1 189280 189280 |
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chrI 29889 29940 c + - supercontig_1.17 -1 189266 189215 |
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chrI 29941 29951 c + i supercontig_1.17 -1 189215 189215 |
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chrI 29989 30098 c + - supercontig_1.17 -1 189200 189091 |
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chrI 30098 30098 c + d supercontig_1.17 -1 189090 189087 |
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chrI 30099 30158 c + - supercontig_1.17 -1 189086 189027 |
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chrI 30159 30159 c + i supercontig_1.17 -1 189027 189027 |
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chrI 30160 30283 c + - supercontig_1.17 -1 189026 188903 |
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chrI 30283 30283 c + d supercontig_1.17 -1 188902 188902 |
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chrI 30297 30297 c + d supercontig_1.17 -1 188887 188887 |
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chrI 30772 30772 c + d supercontig_1.17 -1 188409 188409 |
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chrI 45369 45369 c + d supercontig_1.17 -1 173812 173810 |
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chrI 56889 56889 c + d supercontig_1.17 -1 162290 162290 |
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chrI 58645 58645 c + i supercontig_1.17 -1 160535 160535 |
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chrI 96841 96841 c + d supercontig_1.17 -1 122352 122352 |
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| 188 |
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| 189 |
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| 190 |
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| 191 |
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| 192 |
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| 193 |
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| 196 |
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| 197 |
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| 198 |
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|
| 199 |
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| 200 |
chrI 167113 167113 c + d supercontig_1.17 -1 57981 57981 |
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| 202 |
chrI 167133 167133 c + d supercontig_1.17 -1 57960 57960 |
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| 203 |
chrI 167134 167138 c + - supercontig_1.17 -1 57959 57955 |
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| 204 |
chrI 167138 167138 c + d supercontig_1.17 -1 57954 57954 |
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| 205 |
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| 206 |
chrI 167142 167142 c + d supercontig_1.17 -1 57949 57949 |
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| 207 |
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| 209 |
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| 210 |
chrI 171848 171848 c + d supercontig_1.17 -1 53241 53241 |
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| 211 |
chrI 171849 171870 c + - supercontig_1.17 -1 53240 53219 |
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| 212 |
chrI 171870 171870 c + d supercontig_1.17 -1 53218 53218 |
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| 213 |
chrI 171871 171882 c + - supercontig_1.17 -1 53217 53206 |
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| 214 |
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| 215 |
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| 216 |
chrI 171957 171957 c + i supercontig_1.17 -1 53131 53131 |
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| 218 |
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| 220 |
chrI 171975 171975 c + i supercontig_1.17 -1 53116 53116 |
|
| 221 |
chrI 171976 171976 c + - supercontig_1.17 -1 53115 53115 |
|
| 222 |
chrI 171977 171977 c + i supercontig_1.17 -1 53115 53115 |
|
| 223 |
chrI 171978 171982 c + - supercontig_1.17 -1 53114 53110 |
|
| 224 |
chrI 171983 171983 c + i supercontig_1.17 -1 53110 53110 |
|
| 225 |
chrI 171984 172016 c + - supercontig_1.17 -1 53109 53077 |
|
| 226 |
chrI 172017 172017 c + i supercontig_1.17 -1 53077 53077 |
|
| 227 |
chrI 172018 172019 c + - supercontig_1.17 -1 53076 53075 |
|
| 228 |
chrI 172020 172020 c + i supercontig_1.17 -1 53075 53075 |
|
| 229 |
chrI 172021 172041 c + - supercontig_1.17 -1 53074 53054 |
|
| 230 |
chrI 172041 172041 c + d supercontig_1.17 -1 53053 53053 |
|
| 231 |
chrI 172042 172042 c + - supercontig_1.17 -1 53052 53052 |
|
| 232 |
chrI 172042 172042 c + d supercontig_1.17 -1 53051 53051 |
|
| 233 |
chrI 172043 172171 c + - supercontig_1.17 -1 53050 52922 |
|
| 234 |
chrI 172171 172171 c + d supercontig_1.17 -1 52921 52921 |
|
| 235 |
chrI 172172 172426 c + - supercontig_1.17 -1 52920 52666 |
|
| 236 |
chrI 172426 172426 c + d supercontig_1.17 -1 52665 52665 |
|
| 237 |
chrI 172427 172433 c + - supercontig_1.17 -1 52664 52658 |
|
| 238 |
chrI 172434 172434 c + i supercontig_1.17 -1 52658 52658 |
|
| 239 |
chrI 172435 175305 c + - supercontig_1.17 -1 52657 49787 |
|
| 240 |
chrI 175305 175305 c + d supercontig_1.17 -1 49786 49786 |
|
| 241 |
chrI 175306 175370 c + - supercontig_1.17 -1 49785 49721 |
|
| 242 |
chrI 175371 175371 c + i supercontig_1.17 -1 49721 49721 |
|
| 243 |
chrI 175372 175807 c + - supercontig_1.17 -1 49720 49285 |
|
| 244 |
chrI 175808 175808 c + i supercontig_1.17 -1 49285 49285 |
|
| 245 |
chrI 175809 175854 c + - supercontig_1.17 -1 49284 49239 |
|
| 246 |
chrI 175855 175855 c + i supercontig_1.17 -1 49239 49239 |
|
| 247 |
chrI 175856 177136 c + - supercontig_1.17 -1 49238 47958 |
|
| 248 |
chrI 177136 177136 c + d supercontig_1.17 -1 47957 47957 |
|
| 249 |
chrI 177137 178600 c + - supercontig_1.17 -1 47956 46493 |
|
| 250 |
chrI 178601 178601 c + i supercontig_1.17 -1 46493 46493 |
|
| 251 |
chrI 178602 178618 c + - supercontig_1.17 -1 46492 46476 |
|
| 252 |
chrI 178618 178618 c + d supercontig_1.17 -1 46475 46475 |
|
| 253 |
chrI 178619 178637 c + - supercontig_1.17 -1 46474 46456 |
|
| 254 |
chrI 178638 178638 c + i supercontig_1.17 -1 46456 46456 |
|
| 255 |
chrI 178639 178766 c + - supercontig_1.17 -1 46455 46328 |
|
| 256 |
chrI 178767 178769 c + i supercontig_1.17 -1 46328 46328 |
|
| 257 |
chrI 178770 179144 c + - supercontig_1.17 -1 46327 45953 |
|
| 258 |
chrI 179144 179144 c + d supercontig_1.17 -1 45952 45951 |
|
| 259 |
chrI 179145 179223 c + - supercontig_1.17 -1 45950 45872 |
|
| 260 |
chrI 179224 179224 c + i supercontig_1.17 -1 45872 45872 |
|
| 261 |
chrI 179225 179978 c + - supercontig_1.17 -1 45871 45118 |
|
| 262 |
chrI 179978 179978 c + d supercontig_1.17 -1 45117 45117 |
|
| 263 |
chrI 179979 180121 c + - supercontig_1.17 -1 45116 44974 |
|
| 264 |
chrI 180121 180121 c + d supercontig_1.17 -1 44973 44972 |
|
| 265 |
chrI 180122 180133 c + - supercontig_1.17 -1 44971 44960 |
|
| 266 |
chrI 180134 180137 c + i supercontig_1.17 -1 44960 44960 |
|
| 267 |
chrI 180138 180163 c + - supercontig_1.17 -1 44959 44934 |
|
| 268 |
chrI 180163 180163 c + d supercontig_1.17 -1 44933 44933 |
|
| 269 |
chrI 180164 180217 c + - supercontig_1.17 -1 44932 44879 |
|
| 270 |
chrI 180218 180218 c + i supercontig_1.17 -1 44879 44879 |
|
| 271 |
chrI 180219 180273 c + - supercontig_1.17 -1 44878 44824 |
|
| 272 |
chrI 180274 180275 c + i supercontig_1.17 -1 44824 44824 |
|
| 273 |
chrI 180276 180827 c + - supercontig_1.17 -1 44823 44272 |
|
| 274 |
chrI 180827 180827 c + d supercontig_1.17 -1 44271 44271 |
|
| 275 |
chrI 180828 180879 c + - supercontig_1.17 -1 44270 44219 |
|
| 276 |
chrI 180880 180880 c + i supercontig_1.17 -1 44219 44219 |
|
| 277 |
chrI 180881 180961 c + - supercontig_1.17 -1 44218 44138 |
|
| 278 |
chrI 180961 180961 c + d supercontig_1.17 -1 44137 44134 |
|
| 279 |
chrI 180962 180967 c + - supercontig_1.17 -1 44133 44128 |
|
| 280 |
chrI 180967 180967 c + d supercontig_1.17 -1 44127 44127 |
|
| 281 |
chrI 180968 181080 c + - supercontig_1.17 -1 44126 44014 |
|
| 282 |
chrI 181080 181080 c + d supercontig_1.17 -1 44013 44013 |
|
| 283 |
chrI 181081 181123 c + - supercontig_1.17 -1 44012 43970 |
|
| 284 |
chrI 181257 181956 c + - supercontig_1.17 -1 43198 42499 |
|
| 285 |
chrI 181957 181958 c + i supercontig_1.17 -1 42499 42499 |
|
| 286 |
chrI 181959 182610 c + - supercontig_1.17 -1 42498 41847 |
|
| 287 |
chrI 182611 182955 c + i supercontig_1.17 -1 41847 41847 |
|
| 288 |
chrI 182956 183381 c + - supercontig_1.17 -1 41846 41421 |
|
| 289 |
chrI 183382 183382 c + i supercontig_1.17 -1 41421 41421 |
|
| 290 |
chrI 183383 183560 c + - supercontig_1.17 -1 41420 41243 |
|
| 291 |
chrI 183560 183560 c + d supercontig_1.17 -1 41242 41242 |
|
| 292 |
chrI 183561 183618 c + - supercontig_1.17 -1 41241 41184 |
|
| 293 |
chrI 183618 183618 c + d supercontig_1.17 -1 41183 41183 |
|
| 294 |
chrI 183619 183620 c + - supercontig_1.17 -1 41182 41181 |
|
| 295 |
chrI 183620 183620 c + d supercontig_1.17 -1 41180 41180 |
|
| 296 |
chrI 183621 184637 c + - supercontig_1.17 -1 41179 40163 |
|
| 297 |
chrI 184637 184637 c + d supercontig_1.17 -1 40162 40161 |
|
| 298 |
chrI 184638 184713 c + - supercontig_1.17 -1 40160 40085 |
|
| 299 |
chrI 184714 184714 c + i supercontig_1.17 -1 40085 40085 |
|
| 300 |
chrI 184715 184775 c + - supercontig_1.17 -1 40084 40024 |
|
| 301 |
chrI 184775 184775 c + d supercontig_1.17 -1 40023 40023 |
|
| 302 |
chrI 184776 185291 c + - supercontig_1.17 -1 40022 39507 |
|
| 303 |
chrI 185291 185291 c + d supercontig_1.17 -1 39506 39506 |
|
| 304 |
chrI 185292 185801 c + - supercontig_1.17 -1 39505 38996 |
|
| 305 |
chrI 185801 185801 c + d supercontig_1.17 -1 38995 38994 |
|
| 306 |
chrI 185802 186515 c + - supercontig_1.17 -1 38993 38280 |
|
| 307 |
chrI 186515 186515 c + d supercontig_1.17 -1 38279 38279 |
|
| 308 |
chrI 186516 186837 c + - supercontig_1.17 -1 38278 37957 |
|
| 309 |
chrI 186837 186837 c + d supercontig_1.17 -1 37956 37956 |
|
| 310 |
chrI 186838 186872 c + - supercontig_1.17 -1 37955 37921 |
|
| 311 |
chrI 186872 186872 c + d supercontig_1.17 -1 37920 37920 |
|
| 312 |
chrI 186873 187521 c + - supercontig_1.17 -1 37919 37271 |
|
| 313 |
chrI 187647 189039 c + - supercontig_1.17 -1 37172 35780 |
|
| 314 |
chrI 189039 189039 c + d supercontig_1.17 -1 35779 35779 |
|
| 315 |
chrI 189040 189239 c + - supercontig_1.17 -1 35778 35579 |
|
| 316 |
chrI 189239 189239 c + d supercontig_1.17 -1 35578 35569 |
|
| 317 |
chrI 189240 189357 c + - supercontig_1.17 -1 35568 35451 |
|
| 318 |
chrI 189357 189357 c + d supercontig_1.17 -1 35450 35382 |
|
| 319 |
chrI 189358 189678 c + - supercontig_1.17 -1 35381 35061 |
|
| 320 |
chrI 189678 189678 c + d supercontig_1.17 -1 35060 35060 |
|
| 321 |
chrI 189679 189689 c + - supercontig_1.17 -1 35059 35049 |
|
| 322 |
chrI 189689 189689 c + d supercontig_1.17 -1 35048 35048 |
|
| 323 |
chrI 189690 189703 c + - supercontig_1.17 -1 35047 35034 |
|
| 324 |
chrI 189703 189703 c + d supercontig_1.17 -1 35033 35033 |
|
| 325 |
chrI 189704 189742 c + - supercontig_1.17 -1 35032 34994 |
|
| 326 |
chrI 189743 189744 c + i supercontig_1.17 -1 34994 34994 |
|
| 327 |
chrI 189745 189751 c + - supercontig_1.17 -1 34993 34987 |
|
| 328 |
chrI 189751 189751 c + d supercontig_1.17 -1 34986 34986 |
|
| 329 |
chrI 189752 189758 c + - supercontig_1.17 -1 34985 34979 |
|
| 330 |
chrI 189759 189763 c + i supercontig_1.17 -1 34979 34979 |
|
| 331 |
chrI 189764 189817 c + - supercontig_1.17 -1 34978 34925 |
|
| 332 |
chrI 189817 189817 c + d supercontig_1.17 -1 34924 34875 |
|
| 333 |
chrI 189818 189971 c + - supercontig_1.17 -1 34874 34721 |
|
| 334 |
chrI 189971 189971 c + d supercontig_1.17 -1 34720 34720 |
|
| 335 |
chrI 189972 190161 c + - supercontig_1.17 -1 34719 34530 |
|
| 336 |
chrI 190161 190161 c + d supercontig_1.17 -1 34529 34529 |
|
| 337 |
chrI 190162 192296 c + - supercontig_1.17 -1 34528 32394 |
|
| 338 |
chrI 192297 192301 c + i supercontig_1.17 -1 32394 32394 |
|
| 339 |
chrI 192302 192302 c + - supercontig_1.17 -1 32393 32393 |
|
| 340 |
chrI 192303 192303 c + i supercontig_1.17 -1 32393 32393 |
|
| 341 |
chrI 192304 192334 c + - supercontig_1.17 -1 32392 32362 |
|
| 342 |
chrI 192334 192334 c + d supercontig_1.17 -1 32361 32360 |
|
| 343 |
chrI 192335 192544 c + - supercontig_1.17 -1 32359 32150 |
|
| 344 |
chrI 192544 192544 c + d supercontig_1.17 -1 32149 32145 |
|
| 345 |
chrI 192545 194000 c + - supercontig_1.17 -1 32144 30689 |
|
| 346 |
chrI 194000 194000 c + d supercontig_1.17 -1 30688 30680 |
|
| 347 |
chrI 194001 194026 c + - supercontig_1.17 -1 30679 30654 |
|
| 348 |
chrI 194027 194029 c + i supercontig_1.17 -1 30654 30654 |
|
| 349 |
chrI 194030 196677 c + - supercontig_1.17 -1 30653 28006 |
|
| 350 |
chrI 196678 196678 c + i supercontig_1.17 -1 28006 28006 |
|
| 351 |
chrI 196679 196823 c + - supercontig_1.17 -1 28005 27861 |
|
| 352 |
chrI 196823 196823 c + d supercontig_1.17 -1 27860 27860 |
|
| 353 |
chrI 196824 196866 c + - supercontig_1.17 -1 27859 27817 |
|
| 354 |
chrI 196866 196866 c + d supercontig_1.17 -1 27816 27816 |
|
| 355 |
chrI 196867 196904 c + - supercontig_1.17 -1 27815 27778 |
|
| 356 |
chrI 196905 196905 c + i supercontig_1.17 -1 27778 27778 |
|
| 357 |
chrI 196906 196918 c + - supercontig_1.17 -1 27777 27765 |
|
| 358 |
chrI 196918 196918 c + d supercontig_1.17 -1 27764 27764 |
|
| 359 |
chrI 196919 197605 c + - supercontig_1.17 -1 27763 27077 |
|
| 360 |
chrI 197605 197605 c + d supercontig_1.17 -1 27076 27076 |
|
| 361 |
chrI 197606 197913 c + - supercontig_1.17 -1 27075 26768 |
|
| 362 |
chrI 197913 197913 c + d supercontig_1.17 -1 26767 26767 |
|
| 363 |
chrI 197914 198024 c + - supercontig_1.17 -1 26766 26656 |
|
| 364 |
chrI 198024 198024 c + d supercontig_1.17 -1 26655 26655 |
|
| 365 |
chrI 198025 198624 c + - supercontig_1.17 -1 26654 26055 |
|
| 366 |
chrI 198625 198625 c + i supercontig_1.17 -1 26055 26055 |
|
| 367 |
chrI 198626 198627 c + - supercontig_1.17 -1 26054 26053 |
|
| 368 |
chrI 198627 198627 c + d supercontig_1.17 -1 26052 26051 |
|
| 369 |
chrI 198628 198693 c + - supercontig_1.17 -1 26050 25985 |
|
| 370 |
chrI 198693 198693 c + d supercontig_1.17 -1 25984 25984 |
|
| 371 |
chrI 198694 198702 c + - supercontig_1.17 -1 25983 25975 |
|
| 372 |
chrI 198703 198703 c + i supercontig_1.17 -1 25975 25975 |
|
| 373 |
chrI 198704 198902 c + - supercontig_1.17 -1 25974 25776 |
|
| 374 |
chrI 198902 198902 c + d supercontig_1.17 -1 25775 25775 |
|
| 375 |
chrI 198903 198993 c + - supercontig_1.17 -1 25774 25684 |
|
| 376 |
chrI 198993 198993 c + d supercontig_1.17 -1 25683 25682 |
|
| 377 |
chrI 198994 198998 c + - supercontig_1.17 -1 25681 25677 |
|
| 378 |
chrI 198998 198998 c + d supercontig_1.17 -1 25676 25676 |
|
| 379 |
chrI 198999 199051 c + - supercontig_1.17 -1 25675 25623 |
|
| 380 |
chrI 199051 199051 c + d supercontig_1.17 -1 25622 25622 |
|
| 381 |
chrI 199052 199057 c + - supercontig_1.17 -1 25621 25616 |
|
| b/doc/R_tutorial/data/aligned/TF/sample_1_TF.txt | ||
|---|---|---|
| 1 |
1 38 F 1 |
|
| 2 |
1 67 F 1 |
|
| 3 |
1 163 F 1 |
|
| 4 |
1 171 F 2 |
|
| 5 |
1 173 F 1 |
|
| 6 |
1 177 F 2 |
|
| 7 |
1 178 F 4 |
|
| 8 |
1 188 F 1 |
|
| 9 |
1 192 F 1 |
|
| 10 |
1 200 F 1 |
|
| 11 |
1 202 F 1 |
|
| 12 |
1 203 F 1 |
|
| 13 |
1 552 F 1 |
|
| 14 |
1 578 F 1 |
|
| 15 |
1 785 F 1 |
|
| 16 |
1 792 F 1 |
|
| 17 |
1 804 F 1 |
|
| 18 |
1 966 F 2 |
|
| 19 |
1 971 F 1 |
|
| 20 |
1 1084 F 1 |
|
| 21 |
1 1105 F 1 |
|
| 22 |
1 1109 F 1 |
|
| 23 |
1 1253 F 1 |
|
| 24 |
1 1291 F 1 |
|
| 25 |
1 1299 F 4 |
|
| 26 |
1 1303 F 1 |
|
| 27 |
1 1305 F 4 |
|
| 28 |
1 1317 F 1 |
|
| 29 |
1 1474 F 2 |
|
| 30 |
1 1481 F 3 |
|
| 31 |
1 1482 F 2 |
|
| 32 |
1 1492 F 1 |
|
| 33 |
1 1506 F 6 |
|
| 34 |
1 1507 F 3 |
|
| 35 |
1 1510 F 4 |
|
| 36 |
1 1512 F 1 |
|
| 37 |
1 1513 F 1 |
|
| 38 |
1 1570 F 2 |
|
| 39 |
1 1578 F 1 |
|
| 40 |
1 1579 F 2 |
|
| 41 |
1 1999 F 1 |
|
| 42 |
1 2179 F 1 |
|
| 43 |
1 2180 F 1 |
|
| 44 |
1 2186 F 1 |
|
| 45 |
1 2239 F 1 |
|
| 46 |
1 2245 F 2 |
|
| 47 |
1 2253 F 3 |
|
| 48 |
1 2266 F 2 |
|
| 49 |
1 2267 F 1 |
|
| 50 |
1 2273 F 1 |
|
| 51 |
1 2280 F 2 |
|
| 52 |
1 2297 F 3 |
|
| 53 |
1 2298 F 1 |
|
| 54 |
1 2299 F 4 |
|
| 55 |
1 2303 F 1 |
|
| 56 |
1 2415 F 1 |
|
| 57 |
1 2597 F 1 |
|
| 58 |
1 2627 F 1 |
|
| 59 |
1 2677 F 1 |
|
| 60 |
1 2682 F 1 |
|
| 61 |
1 2687 F 1 |
|
| 62 |
1 2699 F 1 |
|
| 63 |
1 2705 F 3 |
|
| 64 |
1 2719 F 1 |
|
| 65 |
1 2739 F 1 |
|
| 66 |
1 2748 F 1 |
|
| 67 |
1 2750 F 13 |
|
| 68 |
1 2751 F 12 |
|
| 69 |
1 2753 F 1 |
|
| 70 |
1 2755 F 1 |
|
| 71 |
1 2756 F 2 |
|
| 72 |
1 2758 F 1 |
|
| 73 |
1 2759 F 7 |
|
| 74 |
1 2761 F 14 |
|
| 75 |
1 2769 F 2 |
|
| 76 |
1 2771 F 2 |
|
| 77 |
1 2772 F 6 |
|
| 78 |
1 2778 F 1 |
|
| 79 |
1 2783 F 1 |
|
| 80 |
1 2786 F 11 |
|
| 81 |
1 2788 F 3 |
|
| 82 |
1 2791 F 3 |
|
| 83 |
1 2793 F 1 |
|
| 84 |
1 2797 F 2 |
|
| 85 |
1 2798 F 1 |
|
| 86 |
1 2802 F 2 |
|
| 87 |
1 2803 F 1 |
|
| 88 |
1 2805 F 2 |
|
| 89 |
1 2809 F 2 |
|
| 90 |
1 2813 F 1 |
|
| 91 |
1 2817 F 1 |
|
| 92 |
1 2819 F 2 |
|
| 93 |
1 2820 F 7 |
|
| 94 |
1 2822 F 6 |
|
| 95 |
1 2827 F 2 |
|
| 96 |
1 2836 F 1 |
|
| 97 |
1 2841 F 1 |
|
| 98 |
1 2852 F 2 |
|
| 99 |
1 2876 F 1 |
|
| 100 |
1 2888 F 1 |
|
| 101 |
1 2889 F 2 |
|
| 102 |
1 2907 F 3 |
|
| 103 |
1 2917 F 3 |
|
| 104 |
1 2923 F 1 |
|
| 105 |
1 2924 F 1 |
|
| 106 |
1 2929 F 4 |
|
| 107 |
1 2930 F 4 |
|
| 108 |
1 2932 F 3 |
|
| 109 |
1 2933 F 2 |
|
| 110 |
1 2939 F 2 |
|
| 111 |
1 2940 F 1 |
|
| 112 |
1 2943 F 1 |
|
| 113 |
1 2945 F 5 |
|
| 114 |
1 2946 F 2 |
|
| 115 |
1 2950 F 3 |
|
| 116 |
1 2954 F 3 |
|
| 117 |
1 2955 F 3 |
|
| 118 |
1 2960 F 1 |
|
| 119 |
1 2961 F 1 |
|
| 120 |
1 2962 F 2 |
|
| 121 |
1 2963 F 5 |
|
| 122 |
1 2967 F 1 |
|
| 123 |
1 2968 F 1 |
|
| 124 |
1 2969 F 1 |
|
| 125 |
1 2972 F 3 |
|
| 126 |
1 2973 F 8 |
|
| 127 |
1 2974 F 2 |
|
| 128 |
1 2975 F 1 |
|
| 129 |
1 2976 F 1 |
|
| 130 |
1 2984 F 3 |
|
| 131 |
1 2985 F 4 |
|
| 132 |
1 2988 F 3 |
|
| 133 |
1 2992 F 1 |
|
| 134 |
1 2996 F 1 |
|
| 135 |
1 2998 F 5 |
|
| 136 |
1 3000 F 1 |
|
| 137 |
1 3003 F 1 |
|
| 138 |
1 3012 F 3 |
|
| 139 |
1 3014 F 1 |
|
| 140 |
1 3015 F 3 |
|
| 141 |
1 3022 F 1 |
|
| 142 |
1 3032 F 1 |
|
| 143 |
1 3037 F 1 |
|
| 144 |
1 3039 F 1 |
|
| 145 |
1 3041 F 3 |
|
| 146 |
1 3050 F 2 |
|
| 147 |
1 3051 F 2 |
|
| 148 |
1 3053 F 1 |
|
| 149 |
1 3060 F 1 |
|
| 150 |
1 3064 F 1 |
|
| 151 |
1 3084 F 2 |
|
| 152 |
1 3100 F 1 |
|
| 153 |
1 3103 F 1 |
|
| 154 |
1 3114 F 2 |
|
| 155 |
1 3123 F 1 |
|
| 156 |
1 3124 F 3 |
|
| 157 |
1 3127 F 2 |
|
| 158 |
1 3128 F 2 |
|
| 159 |
1 3133 F 1 |
|
| 160 |
1 3143 F 1 |
|
| 161 |
1 3159 F 1 |
|
| 162 |
1 3161 F 1 |
|
| 163 |
1 3171 F 1 |
|
| 164 |
1 3177 F 1 |
|
| 165 |
1 3179 F 2 |
|
| 166 |
1 3182 F 1 |
|
| 167 |
1 3184 F 3 |
|
| 168 |
1 3185 F 2 |
|
| 169 |
1 3189 F 1 |
|
| 170 |
1 3194 F 1 |
|
| 171 |
1 3195 F 4 |
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| 172 |
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1 5282 F 2 |
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1 5285 F 2 |
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1 5286 F 1 |
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1 5290 F 1 |
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Formats disponibles : Unified diff