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  • Error in contigs length in 454AllContigs.fna 454 Output file

    Hi there,

    Checking out the 454 output file 454AllContigs.fna I've found out some errors in contig length. There are some cases where the contig length written in the fasta header is clearly different from the actual contig length, sometimes bigger, sometimes smaller. An example

    >contig04402 length=72 numreads=580 gene=isogroup00010 status=isotig
    ttgtattgaatgcactgaTCTGGGGTgAGAAATCTTCTGGTGCTgtACCTTTTGGGACTA
    TGTTTGCTTtGGTcTTTTTGtGGTTtGGAATTTCCGTGCccTtGGTTTTTATTGGCAGct
    ACTTTGGCTACAAGAAACCTGCAATTGAagATCCAGTGAAAACAAACAAAATTCCCAGGC
    AAATT



    Does anyone know what could be happening?

    Thanks

    Marina

  • #2
    I have the same problem using newbler with cdna option.
    I have already write to penzberg and they answer me that this is probably a bug

    Comment


    • #3
      Hi pr0t3us,

      thanks very much for your reply. It's good to know it's a bug

      Marina

      Comment


      • #4
        The length is not of contigs, bua of isotigs.
        lenght=72 mean that in the contig04402, only 72bp used in isotigs.
        anywhere... that is just a bug.

        Comment


        • #5
          i also find the bug, but i email to 454 Roche company and don't get the answer.

          Through comparision, the lenght=72 maybe the length longer than another contig from the same isotig. For example, the following is part of Newbler result,contig00919's length is 491, that is right. But, the length of contig02971 is 216, it's error, the actual length of contig02971 is 707, just 491+216=707. The blast result also show the former 491 bp are the same bettween two contig.



          >contig00919 length=491 numreads=9 gene=isogroup00335 status=isotig
          TtGgAGGAGCCAaGGgCATCTCTCTCATACACACAaGCACTATATTATaTGTATATGATT
          GAGCTAAGGCAGTTGCAGGAATTATCTGTGTATaTATTATtATGTACATTATGTTCaTaC
          AaTTAAGTTTAAAAGATGCAACACCTCACCaCTAAACCCTTTTgATCAATCCtCGCCTCA
          TCATTGCCTTCaGGAGGCTGAGTAAGCTTCCGgTTTTgTGGAGACATCATTTCTTTCTtC
          AGCTGAGTCAATATATCCTCCATTGTATaCTCCCTTCGCCAATTAGCAAGCATGGGGAAA
          AGGCTTGGTTCAACCACTTTGGTTTCGGgATTGACACAGGTCATATTTATCCGGGTTTGA
          AACCTCACGCTCGGTGGGTTATCGGgATAATCCATGCCACAGAACAATTTCAACTGGTAG
          ATGCGTCCTtCATGAaCAGTATTAGGgGGgCCgaTAATAGTGCcAGTCCACGATTGCATG
          TATACTtCATC
          >contig02971 length=216 numreads=21 gene=isogroup00335 status=isotig
          TtGgAGGAGCCAaGGgCATCTCTCTCATACACACAaGCACTATATTATaTGTATATGATT
          GAGCTAAGGCAGTTGCAGGAATTATCTGTGTATaTATTATtATGTACATTATGTTCaTaC
          AaTTAAGTTTAAAAGATGCAACACCTCACCaCTAAACCCTTTTgATCAATCCtCGCCTCA
          TCATTGCCTTCaGGAGGCTGAGTAAGCTTCCGgTTTTgTGGAGACATCATTTCTTTCTtC
          AGCTGAGTCAATATATCCTCCATTGTATaCTCCCTTCGCCAATTAGCAAGCATGGGGAAA
          AGGCTTGGTTCAACCACTTTGGTTTCGGgATTGACACAGGTCATATTTATCCGGGTTTGA
          AACCTCACGCTCGGTGGGTTATCGGgATAATCCATGCCACAGAACAATTTCAACTGGTAG
          ATGCGTCCTtCATGAaCAGTATTAGGgGGgCCgaTAATAGTGCcAGTCCACGATTGCATG
          TATACTtCATCAGCATCATCCATTCCATAGCTAACAGTTCCATCCCCAATtCcTTTTtCA
          CCTCTCtCgaGTtCTTCtaGCAATCTGAAATTCCtaGGCACAaCAACactcGATCCTTCA
          GAACCCATTCCTTCTcttGATCGTTCAAAAcAAAGAGATtAaGAATtAGGgTTTTTTttC
          TCTGATTTCAAAAGCGAAAgCCCAaAAATAGtaGAGAGGAAAaTCAA

          Comment

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