Unmapped read output

[Former user]

Hi,

can you please add an option to output unmapped reads, this is very important for many applications. The mapped .frag file does not contain read IDs so this can't be used to work out the unmapped reads.

Thanks,

Theo Allnutt

[ptlcc]

Hi Theo

The last field in the *.frag file contains the ID of matched query sequence. Alternatively you can add the argument “-sam”, which will stream sam-format output to stdout.

Best,

Philip

[Theo Allnutt]

I see that now, thanks very much. You can close the issue.

[Mihkel Vaher]

Hi!

I’m also interested in picking out only the unmapped reads (similar to contaminant removal).

Hopefully I misunderstood, but is the only way to get the unmapped reads is to remember all the mapped reads, then go through the fastq again and picking out the ones that are NOT in the mapped list?

Thanks,
Mihkel

[ptlcc]

Hi Mihkel

The easiest way to do that would be to parse the sam output. It is available with the “-sam” option, and will output to stdout.

Best,
Philip