How do you pull a bunch of reads by ID?

[dacotahm]

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?

[GenoMax]

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