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Old 01-11-2015, 04:41 PM   #6
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,061

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
$ in=reads.fq ref=KIR.fa outu=things_that_do_not_match.fq outm=reads_match_KIR.fq
Reads that match things in KIR.fa are collected in "reads_match_KIR.fq" file rest are put in the other file.

If you have paired-end reads:
$ in1=reads1.fq in2=reads2.fq ref=KIR.fa outu1=no_match_1.fq outu2=no_match_2.fq outm1=matched_to_KIR1.fq outm2=matched_to_KIR_2.fq
Note: This should definitely work with a single KIR sequence file (it also may work with a multi-fasta file). Give it a try and see what happens.
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