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3 hours ago by

European Union

This might be a stupid question, but I have to figure this out ->
I want to get unaligned reads when I run bowtie2

I tried every variation of --un I could think of. For example, I found this option in biostars:

bowtie2 -t -p 2 -q --phred33-quals --mm -x Human_rRNA -1 R1.fq -2 R2.fq -S out.sam  --un unaligned.sam

This didn't work - I tried moving the --un location, giving a directory, specifying file name (/unaligned/unaligned.fq) using --un-gz
All this didn't work

Then I tried --un-conc and now I get out files

bowtie2 -t -p 2 -q --phred33-quals --mm -x Human_rRNA -1 R1.fq -2 R2.fq -S out.sam  --un-conc unaligned.sam

But is it the same as unaligned?
I essentially want samtools -f 4 reads, in the original pairs

Any elucidation will be most welcome

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3 hours ago
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blur160



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