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Forum: Bioinformatics 01-11-2015, 04:41 PM
Replies: 6
Views: 1,752
Posted By GenoMax
If your KIR files are in fasta format then here...

If your KIR files are in fasta format then here is what you do (command only for reference, make appropriate changes as needed):

If you have single end reads

$ bbsplit.sh in=reads.fq ref=KIR.fa...
Forum: Bioinformatics 01-11-2015, 04:00 PM
Replies: 6
Views: 1,752
Posted By GenoMax
Can you elaborate as to what "database" here...

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...
Forum: Bioinformatics 01-08-2015, 05:10 PM
Replies: 6
Views: 1,752
Posted By GenoMax
kir == Killer cell immunoglobulin-like receptors...

kir == Killer cell immunoglobulin-like receptors (KIRs) genes? Why not get the sequences you are interested in, use BBSplit (http://seqanswers.com/forums/showthread.php?t=41288) to fish out the...
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