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bowtie2 --un option problems

Hi, I am trying to use the bowtie2 --un option, but I must be doing something wrong because the un-seq file appears to be empty. the manual says to write --un <path> : should it include an outfile name? i.e. /path/to/un/file.fastq? or is it /path/to/file/ ? Thanks!

bowtie2
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updated by Matteo Schiavinato Matteo Schiavinato • written by blur blur

Try using --un-conc as well, maybe it's paired.

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written by Asaf Asaf

a followup question - I tried --un /path/test and --un-conc /path/test2 and I got the outfiles: test.1 test.2 am I right to assume that the --un option didn't work while --un-conc did (so, it was paired-end reads)? Because the manual says for --un-conc: "Write paired-end reads that fail to align concordantly to file(s) at <path>. These reads correspond to the SAM records with the FLAGS 0x4 bit set and either the 0x40 or 0x80 bit set (depending on whether it's mate #1 or #2). .1 and .2 " Thanks!

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written by blur blur

1 answer

You should specify a file, completely. In the manual, this is described quite accurately.

http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#output-options

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written by Matteo Schiavinato Matteo Schiavinato

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