refmap empty

[madsaan]

Hi ,

My cufflinks and cuffcompare commands are as follows.For some reason my refmap file is empty except for the header file.The chr name in both files are the same.not sure why it is not finding any matches.



cufflinks -F 0.15 -p 6 -L gonad -o ./cufflinks_output /data/tophat_ens/accepted_hits.sam


cuffcompare -r Canis_familiaris.BROADD2.60.gtf -s /data/chr/ -o cuffcompare_tophat /data/ms2374/cufflinks_output/transcripts.gtf

Your help will be greatly appreciated.

Thanks,
Joji

[madsaan]

I figured out why I was getting no matches.The chr is represented as Un,X ,1 etc instead of chrUn and so on.After fixing that am getting a warning saying " found 59 transcripts with undetermined strand." Am not sure as to what is going on.any help will be greatly appreciated.