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Old 01-20-2012, 08:35 AM   #1
tboothby
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Location: DC

Join Date: May 2011
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Default Tophat -> Cuffdiff missing sequences

Hi all. I am hoping you guys can help me with an issue, I apologize for my newbish-ness ahead of time, I am still trying to learn the software.

Background:
I run tophat/bowtie on a RNAseq sample and check the accepted_hits.bam file for "sequenceX" in IGV. I find that sequenceX has good coverage in my sample.

I use this accepted_hits.bam file with cufflinks. I check the transcripts.gtf file for sequenceX and find it is not there.

Question:
Does this make sense? Why would this be happening? Maybe I am not understanding how the software works, but I thought if I provided a reference for sequenceX and have RNAseq data with fragments fully covering sequenceX, that I should get sequenceX being assembled by cufflinks.

In addition:
I have used the exact same RNAseq data with Trinity to de novo assemble a transcriptome and sequenceX is assembled perfectly.
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Old 06-20-2013, 07:34 AM   #2
dekkers
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Default

Did you ever find an answer to this question? I am having the same problem.
Thanks!
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