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  • tophat 1.1.4 bam file

    When I convert the bam file from the output of tophat 1.1.4 to a sam file, it loses the strand specificity ie,, XS:A+/- at the end. This renders it unusable for cufflinks. The conversion I used is samtools view -h -o out.sam in.bam. Any suggestions?

  • #2
    The latest version of cufflinks directly accepts the bam file produced by TopHat. you do not need to conver the bam file into sam file. I just did this a couple of days ago.

    $./cufflinks -G refGene.gtf accepted_hits.bam

    This works quite well

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    • #3
      I am having a similar problem with converted output .sam files. And when I input my .bam directly into cufflinks, I get the following within a second before the process terminates:

      Counting hits in map
      CIGAR op has zero length
      CIGAR op has zero length
      CIGAR op has zero length
      Total map density: 0.000000
      CIGAR op has zero length
      CIGAR op has zero length
      CIGAR op has zero length
      Do .bam files have a CIGAR string? Has anyone else encountered this problem?

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