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Old 08-01-2012, 07:49 AM   #6
mmanrique
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Location: Granada, Spain

Join Date: Dec 2009
Posts: 12
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Hi,

we had the same problem and tried the new Cufflinks version 2.0.2 and it seems the values from Cufflinks and Cuffdiff are the same (have to check it more carefully)

these are the commands I used

Code:
cufflinks -o ./Sample001_cufflinks_out_No_N_2.0.2 -u -g ../genes.gtf -p 2 --total-hits-norm ../Sample_001_accepted_hits.bam
Code:
cuffdiff -o ./COMPARISON1_SAMPLE1_SAMPLE1BIS_cuffdiff_out/ -L SAMPLE1,SAMPLE1BIS -p 2 -u -v -emit-count-tables -total-hits-norm ../Sample001_cufflinks_out/transcripts.gtf ../Sample_001_accepted_hits.sam ../Sample_001_bis_accepted_hits.sam
I know it's weird to use cuffdiff to compare one sample to itself but I had no other choice...

HTH

Marina

EDIT: Though the FPKM values from Cufflinks and Cuffdiff are now more similar I still get unreasonable high FPKM values specially for very short genes (around 37nt, regulatory RNAs I guess). Searching for some kind of explanation I found this thread http://seqanswers.com/forums/showthread.php?t=20702 it's worth reading it, good explanation by Cole Trapnell on why in small genes you can get extremely high FPKM values

Last edited by mmanrique; 08-04-2012 at 07:25 AM.
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