Output files

[mi3112]

Hi John

I'm trying to filter out unitigs associated with antibiotic resistance. I used unitig-counter but I am not sure what output file I should use to use pyseer later. Could you specify the use of the files: unitigs.txt.gz and unitigs.unique_rows.Rtab?

[johnlees]

You can use either. Typically I'd recommend using --kmers unitigs.txt.gz with pyseer (just make sure it is gzipped as noted mgalardini/pyseer#132).

But you can also use --pres unitigs.unique_rows.Rtab. The output is a little more difficult to interpret as you need to refer to the unique rows to unitigs mapping to get the sequences back, which is why I'd recommend the above. This file is non-redundant, and can be useful for computing the multiple testing threshold.