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Old 07-29-2013, 01:09 AM   #1
Petrichor
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Default How to extract those reads, that are not fully aligned in BLAST+?

Hi there!

Like the title says, How do i get those reads, that are not fully aligned in BLAST?
Someone already tried it?
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Old 07-29-2013, 04:52 AM   #2
rhinoceros
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What do you mean by fully aligned?
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Old 07-29-2013, 04:59 AM   #3
sBeier
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If you aligned reads against a database, you will have to extract the identifiers of reads that did align to something first and then extract those reads from the original input file. There is no way to fully recover incompletely aligned query sequences from blast output (as far as I am aware).
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Old 07-29-2013, 10:36 AM   #4
TabeaK
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I've been doing something similar recently - mainly via awk command from a tabbed blast+ output and then using this file to filter an input sequence file.

If you elaborate a little on what you are trying to do, I may be able to help.
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