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¶ ↑
Install some prerequisites via conda, and then dirseq itself:
conda create -c bioconda -n dirseq -y ruby samtools bedtools'>'2.24 conda activate dirseq gem install dirseq
The following dependencies are installed above, but for completeness of documentation, dirseq requires these dependencies, on top of the Ruby ones: * 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¶ ↑
Example usage:
Download the example data:
git clone https://github.com/wwood/dirseq cd dirseq
Then run dirseq:
dirseq --bam spec/data/eg.bam --gff spec/data/eg.gff --measure-type count
Full usage help:
$ 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: --forward-read-only consider only forward reads (i.e. read1) and ignore reverse reads. [default false] --ignore-directions ignore directionality, give overall coverage [default: false i.e. differentiate between directions] --measure-type TYPE what to count for each gene [options: count, coverage][default: coverage] --accepted-feature-types TYPE Print only features of these type(s) [default CDS] --comment-fields Print elements from the comments in the GFF file [default ID] --sam-filter-flags Apply these samtools filters [default: -F0x100 -F0x800] 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
Running on EnrichM output, the output columns are changed relative to {PROKKA}[https://github.com/tseemann/prokka]-generated GFF files:
dirseq --bam spec/data/eg.bam --gff spec/data/eg.gff --measure-type count --comment-fields seq_id,annotations
Project home page¶ ↑
Information on the source tree, documentation, examples, issues and how to contribute, see
The BioRuby community is on IRC server: irc.freenode.org, channel: bioruby.
Cite¶ ↑
If you use this software, please cite
Woodcroft, B.J., Singleton, C.M., Boyd, J.A. et al. Genome-centric view of carbon processing in thawing permafrost. Nature 560, 49–54 (2018). doi.org/10.1038/s41586-018-0338-1
Copyright¶ ↑
Copyright © 2014-2021 Ben J. Woodcroft. See LICENSE.txt for further details.