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Old 02-20-2012, 12:10 PM   #1
Xiaomin Yu
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Location: Washington DC

Join Date: Jul 2011
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Default Problems for cuffdiff output FPKM tracking files

I run the cuffdiff for comparing two RNAseq samples as follows:

/usr/local/cufflinks/bin/cuffdiff /ucsc/dm3/genes.gtf /data/RNAseq/Cufflink/Wide-type_3/accepted_hits.bam /data/mutant/accepted_hits.bam

but in the output FPKM tracking files (cds.fpkm_tracking, genes.fpkm_tracking,isoforms.fpkm_tracking, tss_groups.fpkm_tracking) , there are no length and coverage value (column 8 and 9 are "-"). Is there something wrong or I omitted some parameters?
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Old 06-13-2012, 09:49 PM   #2
mafengshou
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I have the same problem
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