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Old 05-18-2021, 01:55 PM   #3
Location: Poland, Warsaw

Join Date: Jan 2013
Posts: 19


so can I write: in1=hds1r1_09clean.fastq.gz,hds1r1_26clean.fastq.gz in2=hds1r2_09clean.fastq.gz,hds1r2_26clean.fastq.gz ... out=s68_to_b73v5.bam


Why I have to use "out" but not "outm"? I want to retain only mapped reads, to keep my file as small as possible.

It is also interesting, why bbwrap haven't alert that options such as "-in1" are invalid. Some output file has been written but I don't know if it is valid. At least bamqc accepted that file. Nevertheless I'd rather want properly generated file, even if it means that I have to wait for it ten days.

Last edited by floem7; 05-18-2021 at 02:02 PM.
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