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Old 01-11-2015, 04:19 PM   #5
arkilis
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Location: Australia

Join Date: Jul 2013
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Quote:
Originally Posted by GenoMax View Post
Can you elaborate as to what "database" here means? You have KIR genes sequences but in what format (plain text, blast, one of NGS aligner index format)?

BBSplit uses alignments to identify reads that map to sequences of interest and then separate them (this can work the other way around as well i.e. you discard reads that map as being uninteresting and collect unmapped reads to process further).
Sorry for the confusion.

KIR gene from www.ebi.ac.uk/ipd/kir in fasta format. I might want to use this as the database to find out how many of them are in the current sequence files. I read some papers online, which says all the sequences (fastq) need to be assemblied first. http://www.nature.com/nrg/journal/v1...l/nrg3174.html

Newbie to this area. Thanks for your advice!

Ben

Last edited by arkilis; 01-11-2015 at 04:39 PM.
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