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Old 02-24-2015, 12:34 PM   #8
vingomez
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Location: USA

Join Date: Sep 2014
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Hi Brian,


Quote:
Originally Posted by Brian Bushnell View Post

For example, if you had a library of something that was contaminated with e.coli and salmonella, you could do this:

For paired reads in 2 files, you would do this:

bbsplit.sh in1=reads1.fq in2=reads2.fq ref=ecoli.fa,salmonella.fa basename=out_%.fq outu1=clean1.fq outu2=clean2.fq

This will produce 3 output files:
out_ecoli.fq (ecoli reads)
out_salmonella.fq (salmonella reads)
clean1.fq and clean2.fq (unmapped reads)


For the example provide above (minor edit for clarity):

(1) Is there a flag/command to generate paired reads for mapped reads (e.g. out_ecoli_r1.fq out_ecoli_r2.fq, out_salmonella_r1 out_salmonella_r2.fq.fq)?

(2) Will this flag/command work with BBMap?


Thanks
Vicente
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