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Old 08-20-2009, 12:09 PM   #1
ewilbanks
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Default 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 at 12:10 PM. Reason: typo
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Old 08-21-2009, 01:25 AM   #2
dawe
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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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