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7.3 years ago
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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!
Try using --un-conc as well, maybe it's paired.
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!
But: how come you don't know if they're paired or single end reads? It's like one of the most important information you can have for mapping accurately your reads (insert size matters: https://www.illumina.com/technology/next-generation-sequencing/paired-end-sequencing_assay.html )