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Old 05-12-2015, 03:20 AM   #13
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,076

If you had used the "--un-conc and --al-conc" options ( the unmapped reads could have been written to separate files when you did the alignment.

1. You could repeat bowtie2 alignment with above parameters added to your original list (easier) OR
2. Identify read ID's of sequences that mapped and use a tool like seqtk to extract the mapped reads (e.g. seqtk subseq in.fq name.lst > out.fq)

Use @Michael.Ante's easy suggestion below

Last edited by GenoMax; 05-12-2015 at 04:34 AM.
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