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  • 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.

  • #2
    Did you ever find an answer to this question? I am having the same problem.
    Thanks!

    Comment

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