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  • How do you pull a bunch of reads by ID?

    Here's what I'm trying to do-

    I'm trying to assemble a couple a candidate genes from a pool of illumina reads. I have a species close to drosophila and would like to align 60 million reads to a transcript from flybase and pull only those reads out and assemble them.

    If I use standalone BLAST I can get csv output but the program only returns aligned portions and I want the whole read. Is there a way to format the output or another way to get the sequence if all I have is a list of IDs?

  • #2
    If you have 60 millions reads then you may want to do this using bwa/samtools.

    Here is a thread that describes how you can extract reads that map using samtools (after you align using bwa): http://seqanswers.com/forums/showthread.php?t=16743

    If you would rather keep using BLAST then see this thread for retrieving specific sequences: http://seqanswers.com/forums/archive...hp/t-8805.html

    This may also help: http://seqanswers.com/forums/showthread.php?t=7241

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