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
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
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