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BED to ELAND/bowtie/MAQ ?

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  • BED to ELAND/bowtie/MAQ ?

    Hi all,

    I'm working with a .bed format file of illumina reads and I don't have the original alignment file. A program I'm working with can read in bowtie, eland, maq or modified bed (see below) but not regular bed files!

    Anyone have a good recommendation for ways to convert .bed to one of these file formats?

    Thanks!!!

    Lizzy
    Last edited by ewilbanks; 08-20-2009, 11:10 AM. Reason: typo

  • #2
    I guess you cannot go back to alignment data, because bed files only retain mapping positions (plus possibly some other information). You may do a couple of things:
    1- simulate alignment data assuming all your reads are perfect matches with fake quality (possibly playing with awk and fasta reading tools)
    2- try to fit your bed into the modified bed.
    Which "modified bed" format are we talking about? How do your data look like?

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