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  • Tophat2: bam file has no quality sequences for a lot of reads

    • With the version 2 of tophat I get an '*' as quality sequences in the bam file for more that 70% of the reads.

      Ex:
      Read 1
      GCCCTCGCGGTGCTCTCCGGGTCTGTGCTGAGGAGAACGCAACTCCGCCG DDDDDDDFFFGHHHJJIJIJIIIJJIGGHIGJJJJJJHGHHHFFFFFCC@
      Read 2
      GGCGTGTGTTGC *
      Read 3
      CCGGCCCTCGCTCCAGCAGCTGGACCCCTACCTGCCGTCTGCTGC *

      Read 4
      CAACTGCTGGCCTGTGCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTTC C@CFFFFFHGHHHIGHJJIIJICEHIGIIIIGHJGIJJJBGDFGGHHIIIH

      The bam file for this same sample with tophat 1.4 is ok.

      Has someone encountered this problem? THank you

  • #2
    Why are your read lengths different. Looks like the two that are the same size have proper quality strings

    Comment


    • #3
      I encountered the same problem.
      Problem was alleviated by switching back to 1.4.1.

      Comment


      • #4
        My reads were filtered for quality. But the same problems happens without filtering. And version 1.4 corrects the problem as mentionned by pzumbo.

        Comment


        • #5
          I'm having the same issue with tophat2. I just posted over here: http://seqanswers.com/forums/showpos...66&postcount=4

          Comment


          • #6
            I had the same problem when running tophat2 with bowtie2. However, I did not see this issue after running tophat2 with the --bowtie1 option. Thus, it might be problem with bowtie2.

            Comment

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