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leekgroup / derfinder

R package for DER Finder, a method for differential expression analysis of RNA-seq data
http://biostatistics.oxfordjournals.org/content/early/2014/01/06/biostatistics.kxt053.short?rss=1
MIT License
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request to modify countReads.py to include strand specific information #5

Closed samirwadhawan closed 10 years ago

samirwadhawan commented 10 years ago

Hi Alyssa,

can you please modify countReads.py so that it can use strand specific RNAseq data.

Thanks so much,

Samir

alyssafrazee commented 10 years ago

a "--stranded" option was added to countReads.py with this commit. If you encounter bugs in the script, please report them. Thanks!

andrewejaffe commented 10 years ago

be aware illumina sometimes reverses the strand labels (no idea why) so there should be an option for saying if your data is reverse-stranded (e.g. fragments off of the + strand are labeled - and visa versa, I saw this in our data and didn't realize this was the case). most read-counting programs have this option, like featureCounts, so maybe the stranded option should be 0 (default), 1 (regular strand-specific), or 2 (reverse strand-specific)

http://bioinf.wehi.edu.au/featureCounts/ "Perform strand-specific read counting (use '-s 2' if reversely stranded):" featureCounts -s 1 -a annotation.gtf -t exon -g gene_id -i mapping_results_SE.bam -o counts.txt

alyssafrazee commented 10 years ago

the reversely-stranded option was added with this commit