search

YeoLab / gscripts

General Use Scripts and Helper functions
MIT License
18 stars 18 forks source link

where is featureCounts? #78

Closed ecwheele closed 8 years ago

ecwheele commented 8 years ago

I have tried two different directories: /projects/ps-yeolab/software/bin/featureCounts

and

/projects/ps-yeolab/software/subread-1.4.5-source/bin/featureCounts

and both times I got the error message: no match.

Where is the current working version of featureCounts?

LeenMachine commented 8 years ago

You can run feature counts like this:

featureCounts -M -a /projects/ps-yeolab/genomes/hg19/gencode_v19/gencode.v19.annotation.gtf -o youroutfile.txt *sorted.bam

you just need to specify if you want multimapping -M the annotation file -a your output file -o

run it in the dir containing your sorted.bam files depending on how many files you have, you may want to login to a node

On Fri, Jul 31, 2015 at 2:15 PM, ecwheele notifications@github.com wrote:

I have tried two different directories: /projects/ps-yeolab/software/bin/featureCounts

and

/projects/ps-yeolab/software/subread-1.4.5-source/bin/featureCounts

and both times I got the error message: no match.

Where is the current working version of featureCounts?

— Reply to this email directly or view it on GitHub https://github.com/YeoLab/gscripts/issues/78.