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  • Multi-read problem with bowtie and cufflinks

    Hi,

    I am trying to use the sorted BAM files (samtools) from bowtie alignments with cuffdiff.

    Although I allow bowtie to report multiple matching reads cuffdiff reports:
    Multi-Reads: 0

    The same cuffdiff parameters used for a TopHat alignment of the same data does show Multi-Reads!

    Any ideas what could be the problem?

    Thanks a lot!

  • #2
    Did you find the solution.

    I had the same problem as you posted last year on this forum.
    I wonder if you found the solution how to deal with the multi-read in bam file generated by Bowtie.
    Thanks.

    Comment


    • #3
      There seem to be some people interested as this post has 434 views but no replies.

      So I investigated the matter and found the following:
      Cuffdiff needs a certain nomenclature for multi-reads in the BAM file. This nomenclature is non-standard (at least for bowtie alone) but done by TopHat automatically. What TopHat basically does is to connect the multireads and make the analysis for cufflinks easier.

      At the moment I use TopHat with a GTF file for my reference transcripts and use this output for cufflinks. This is quite quick and does the job.

      I wished the tuxedo-suite developers cared more for their users and give this information somewhere ...

      hope this helps,

      Comment


      • #4
        Thanks~

        Thank you very much for the information.
        Recently launched Bowtie2 generates much sensitive alignment compared to the previous Bowtie. So, I tried to avoid using Tophat because it still uses old Bowtie for its process.

        Comment

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