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bacpop / unitig-counter

Uses cDBG to count unitigs in bacterial populations
GNU Affero General Public License v3.0
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Output files #11

Open mi3112 opened 3 years ago

mi3112 commented 3 years ago

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 commented 3 years ago

You can use either. Typically I'd recommend using --kmers unitigs.txt.gz with pyseer (just make sure it is gzipped as noted https://github.com/mgalardini/pyseer/issues/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.