dirseq

DirSeq work out whether RNAseq reads from metatranscriptomes are generally in the same direction as the ORF predicted, and provide gene-wise coverages using DNAseq mappings.

Note: this software is under active development!

Installation

Won't work just yet:

gem install dirseq

Requires:

samtools (tested with 0.1.19 and 1.0+)
bedtools (tested with 2.24.0) - old versions won't work.
Ruby (tested with 2.1.1)

Usage

Only the script is available at the moment

$ dirseq -h

    Usage: dirseq <arguments>

    Reports the coverage of a mapping in against each gene given in a GFF file

        --bam FILE                   path to mapping file [required]
        --gff FILE                   path to GFF3 file [required]

Optional parameters:

        --ignore-directions          ignore directionality, give overall coverage [default: false i.e. differentiate between directions]

Verbosity:

    -q, --quiet                      Run quietly, set logging to ERROR level [default INFO]
        --logger filename            Log to file [default stderr]
        --trace options              Set log level [default INFO]. e.g. '--trace debug' to set logging level to DEBUG

Project home page

Information on the source tree, documentation, examples, issues and how to contribute, see

http://github.com/wwood/dirseq

The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.

Cite

If you use this software, please cite one of

Biogems.info