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  • IMAGE2 input and parameters

    I am able to run IMAGE2 after creating read.placed.original and contigs.fa.original in the required format. Here are my questions:
    * Is it possible to supply multiple insert libraries to IMAGE? If yes, how?
    * What is the difference between "insert size" and "velvet ins_len" in submit.iteration_.log?
    * I am working with a bacterial genome. So I assume that all contigs will go into Supercontig1 in read.placed.original. Is that correct?

    Please let me know if any question is unclear. Is there a IMAGE mailing list? I was not able to find one on the sourceforge project page. Thanks

    -Surya

  • #2
    Here is what I learned from the authors
    * Is it possible to supply multiple insert libraries to IMAGE? If yes, how?
    No
    * What is the difference between "insert size" and "velvet ins_len" in submit.iteration_.log?
    insert size is the mapping parameter used in ssaha or bwa. velvet ins_len is the insert size used in velvet.
    * I am working with a bacterial genome. So I assume that all contigs will go into Supercontig1 in read.placed.original. Is that correct?
    Yes

    -Surya

    Comment


    • #3
      good job~thx

      Comment


      • #4
        I am looking for some more info on "insert size" and "velvet ins_len". It is not clear which is used for what?

        My additional Illumina data have a insert size of 260.

        I can set "velvet ins_len" as a parameter to 000_walk_all_raw.pl, but where is "insert size" set?

        (IMAGE2 would benefit from a bit more documentation).


        Cheers


        Martin

        Comment

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