temehi / fx_tools Goto Github PK

                                   FX Tools
                         NGS Data Manipluation Tools

                                 Version 0.2
                                 August, 2013

------------------------------------------------------------------------------
Table of Contents
------------------------------------------------------------------------------

  1. Overview
  2. Examples
  3. Reference and Contact

------------------------------------------------------------------------------
1. Overview
------------------------------------------------------------------------------

------------------------------------------------------------------------------
2. Examples
------------------------------------------------------------------------------

------------------------------------------------------------------------------
2.1 Help
------------------------------------------------------------------------------

You can get the manual for the tools by calling them with the --help command,
for example:

$ fx_bam_coverage --help

prints the help of fx_bam_coverage.

------------------------------------------------------------------------------
2.2 Coverage computation of SAM or BAM file
------------------------------------------------------------------------------

$ fx_bam_coverage

------------------------------------------------------------------------------
3. Reference and Contact
------------------------------------------------------------------------------

Send an email to the SeqAn mailing list:

    https://lists.fu-berlin.de/listinfo/seqan-dev

------------------------------------------------------------------------------
4. R Snippets
------------------------------------------------------------------------------

------------------------------------------------------------------------------
4.1. Conversion for Plotting with R
------------------------------------------------------------------------------

Converting the data.frame generated from the fx_fastq_stats TSV output into
a list that can be plotted using bxp(R).

    colnames(R) <- c("Column", "Count", "Minimal.Quality", "Maximal.Quality",
                     "Quality.Sum", "Quality.Mean", "1st.Quartile.Score",
                     "Median.Score", "3rd.Quartile.Score",
                     "Inter.Quality.Range", "Left.Whisker", "Right.Whisker",
                     "A.Count", "C.Count", "G.Count", "T.Count", "N.Count")
    stats <- t(data.matrix(R[c("Minimal.Quality", "1st.Quartile.Score",
                               "3rd.Quartile.Score", "Maximal.Quality")]))
    n <- R[, "Count"]
    conf <- t(data.matrix(R[c("Minimal.Quality", "Maximal.Quality")]))
    out <- c()
    group <- c()
    names <- c()
    R <- list(stats=stats, n=n, conf=conf, out=out, group=group, names=names)