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  • input files for IMAGE

    Hi everybody,

    I'm currently working on the assembly of two bacterial genome sequences from an illumina GAIIx sequencer. I have made a de novo assembly of the 50bp paired end reads with velvet and now would like to try to close some gaps with IMAGE.


    In the very short description of IMAGE i found the following necessary input files:
    a contigs.fa.original file in FASTA format.
    a read.placed.original file containing a list of contigs within supercontigs.
    Paired end Illumina fastq files (should be unzipped)


    From Velvet I got the contigs.fa file and I have Paired end fastq files, but from which program will I get a read.placed.original file? Or did I miss some options for velvet?

    I'm still quite new in the field of bioinformatics and not used to use linux, so could you please explain everything very simple

    Thanks,
    Maegwin

  • #2
    You need to write a simple script with perl to produce a read.placed.original file in the format that comes with the example file.

    Comment


    • #3
      Ok, so actually I never wrote a script, so how to do this?
      I will check on some Online-Tutorials on how to write a Pearl Script.

      Comment


      • #4
        Originally posted by KanyeDidIt View Post
        You need to write a simple script with perl to produce a read.placed.original file in the format that comes with the example file.
        I don't know the corresponding between contigs and scaffold contigs. how do I write script? what is the input of this script?

        Comment


        • #5
          Originally posted by gridbird View Post
          I don't know the corresponding between contigs and scaffold contigs. how do I write script? what is the input of this script?
          If the contigs are in Pcap format its kind of easy to indentify the contig - scaffold relationship.

          Contig5.1, Contig5.2..... should belong to Scaffold5. Something similar to that. This can be customizable for other formats if you have scaffolding information I guess.

          Comment

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