Read Counts Difference From Different Tools
Hi, I got reads counts from rnaseq from different tools, I am not sure why the cufflinks gives so different counts result. Anyone have experience on that?
ACTB 40264.3 38071.2 26648.7 41528.2 39006.5 40361.8 47723.2 25179.8 cufflinks
ACTB 2889 1102 1793 2264 2747 1836 624 2316 htseq
ACTB 2084 875 1362 1719 1919 1345 475 1722 partek
Thanks, Cam
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Check this post Deseq, Edger And Cuffdiff - Different Result, might give some hints :)
Is that the correct link? I do not see that phrase, nor anything which answers this question.
now corrected !!
I think it was about differential expression, and that the problems were eventually with cuffdiff, not cufflinks. I think Cam's problem is at the read count estimation stage.
You can check these links:
How did you run cufflinks? Its estimates are orders of magnitudes higher than the other tools.
Thanks, I run cuffdiff like this: "cuffdiff -p 8 --uper-quartile-norm -u -b hg19.fa -o output merged.gtf s1.bam s2.bam s3.bam ..."
Cam, could you try to run cuffdiff without the quartile normalizatioin?
Hi massyah, I tried with no --uper-quartile-norm option and got the same result... So I think the problem might not be here..
Could it be that cufflinks returns FPKM and htseq and partek return the other two read counts? I just read the htseq man page here http://www-huber.embl.de/users/anders/HTSeq/doc/count.html#count (I never used the software so ... beware!) and I think I understood that the software actually count the reads mapping, and not FPKM. I don't know what partek does. You can track read counts in cuffdiff output files such as "genes.count_tracking", but I never didi it.