View Single Post
Old 01-12-2015, 08:47 PM   #7
arkilis
Senior Member
 
Location: Australia

Join Date: Jul 2013
Posts: 119
Default

Quote:
Originally Posted by GenoMax View Post
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
Code:
$ bbsplit.sh 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:
Code:
$ bbsplit.sh 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.
Finally I used the command you suggested:

bbsplit.sh in1=read1.fastq in2=read2.fastq ref=KIR_nuc.fasta outu1=no_match_1.fq outu2=no_match_2.fq outm1=matched_to_KIR1.fq outm2=matched_to_KIR2.fq

Will discuss with colleagues and get back Thanks!
arkilis is offline   Reply With Quote