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  • Tophat and Bowtie results

    i have reads.fq (5 000 000 reads RNA-seq) genome.fa

    when i use bowtie align the reads, it aligns 4 200 000 reads.

    but when i use tophat align the reads, the output file accepted_hits.sam only contains 1 900 000 reads. junctions.bed file is blank.

  • #2
    Hi,
    Could you tell me the parameters you set?

    Comment


    • #3
      default parameter


      tophat ref.fasta reads.fq

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      • #4
        I also have similar question of inconsistent number of mapping, probably because the parameter setting. Any suggestion about setting the parameter in bowtie/tophat so I can take advantage of the long reads while allowing more mismatches. The /tmp/segments_juncs.fa only have 45bp. How can I use longer reads to map to the junction?

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        • #5
          Hello,
          You can send E-mail to Cole Trapnell([email protected]). He is the author of TopHat and Bowtie.

          All the best,

          Geng

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          • #6
            Hello,
            You can email Cole Trapnell([email protected]).He is the author of TopHat and Bowtie.

            All the best,

            Geng

            Comment


            • #7
              Thanks, and sorry about the late response. I was told (and confirmed by the options) that Tophat cut long reads into smaller pieces to find junction. In this way, 45 bp junctions will be enough. I think the design is try to avoid there are super small exon that is smaller than 45 bp. If so, a 100 bp reads may mapped to 3 exons.

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