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  • tophat: option --read-gap-length not recognized?

    Hi,

    I'm really new to this so please bear with me if I made some really silly mistakes.

    Here's my code for tophat:
    tophat -p 8 --bowtie1 -G path --no-novel-juncs --read-mismatches 4 --read-gap-length 3 --read-edit-dist 2 -o path path &

    and it gave me error :
    tophat: option --read-gap-length not recognized

    Any advice'd be appreciated thanks!
    Last edited by eric.yu; 07-10-2013, 01:11 PM.

  • #2
    1) What version of tophat are you running.....are you sure you have tophat2? Try typing tophat --version to see what version you have.

    2) Secondly, that command wouldn't work anyhow. --read-mismatches and --read-gap-length cannot exceed the value of --read-edit-dist. If you want to set the read-mismatches to 4 an --read-gap-length to 3, then you also have to set the read-edit-dist to 4 or more.
    Last edited by chadn737; 07-10-2013, 03:16 PM.

    Comment


    • #3
      Originally posted by chadn737 View Post
      1) What version of tophat are you running.....are you sure you have tophat2? Try typing tophat --version to see what version you have.

      2) Secondly, that command wouldn't work anyhow. --read-mismatches and --read-gap-length cannot exceed the value of --read-edit-dist. If you want to set the read-mismatches to 4 an --read-gap-length to 3, then you also have to set the read-edit-dist to 4 or more.

      Thanks for your reply.
      It's 2.0.4
      and also tried
      tophat -p 8 --bowtie1 -G $home/Genes/genes.gtf --no-novel-juncs --read-mismatches 4 --read-gap-length 3 --read-edit-dist 4 -o $home/C1_thout3 $home/BowtieIndex/genome $home/Sample_C1.R1_trimmed.fq.gz &

      still doesn't run

      Comment


      • #4
        Hi Senior Member
        I have used tophat successfully with default functions. however, this time I got problem. How to give commands for read length 101 x 2 with insert sixe 80~380(main 150) ?
        I am totally confused


        Originally posted by chadn737 View Post
        1) What version of tophat are you running.....are you sure you have tophat2? Try typing tophat --version to see what version you have.

        2) Secondly, that command wouldn't work anyhow. --read-mismatches and --read-gap-length cannot exceed the value of --read-edit-dist. If you want to set the read-mismatches to 4 an --read-gap-length to 3, then you also have to set the read-edit-dist to 4 or more.

        Comment


        • #5
          Originally posted by jp. View Post
          Hi Senior Member
          I have used tophat successfully with default functions. however, this time I got problem. How to give commands for read length 101 x 2 with insert sixe 80~380(main 150) ?
          I am totally confused
          I presume that you've looked at --mate-inner-distance plus --mate-std-dev and are just having a hard time figuring out that the numbers should be. Here are two relevant seqanswer posts that should help:

          Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc


          and

          Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc

          Comment


          • #6
            Thank you so much for your help. I got the answer. negative value can be given for --mate-inner-distance.
            Great help for me, thanks


            Originally posted by westerman View Post
            I presume that you've looked at --mate-inner-distance plus --mate-std-dev and are just having a hard time figuring out that the numbers should be. Here are two relevant seqanswer posts that should help:

            Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc


            and

            http://seqanswers.com/forums/showthread.php?t=4355

            Comment

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