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  • Tophat paired end alignment help: comma or blank to separate two pairs?

    Hi All,
    I am using the current command to run a PE alignment in Tophat:
    $ tophat -p 4 -m 2 -r 200 /index/hg19 /data/raw/N1_1.fa,N1_2.fa

    my question is, both N1_1.fa and N1_2.fa are the paired end reads generated from a single human tissue sample. Should I use comma or blank to separate those two? And here is the log for the alignment, is 76% alignment looks normal? Thanks!

    # reads processed: 242980185
    # reads with at least one reported alignment: 185782139 (76.46%)
    # reads that failed to align: 56208030 (23.13%)
    # reads with alignments suppressed due to -m: 990016 (0.41%)
    Reported 457696000 alignments to 1 output stream(s)

  • #2
    a space between file_1 and file_2.

    Comment


    • #3
      @jbrwn
      Thanks! Hope that improves my alignment rate.

      Comment


      • #4
        Originally posted by mediator View Post
        @jbrwn
        Thanks! Hope that improves my alignment rate.
        i typically include --mate-std-dev <int> as well, though i'm not sure how much difference it makes. this information should be available from the bioanalyzer output or someone-from-the-lab output.

        Comment

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