Get reads assigned to a particular species

[Danieljaen]

I was wondering if it is possible to get a file with only the reads that has been assigned to a particular species in the output. Or, at least, a list of the especific reads that has been assigned to it, so I can extract them myself from the original fastq files afterwards.

[fwa93]

Hi,
Right now you can get a list where each read has a sort of probability assignment for each species. Use the flag "-- keep_read_assignments" to get this list.
"output .tsv file with read assignment distributions: each row as an input read; each entry as the likelihood it is dervied from that taxa (taxid is the column header); each row sums to 1" https://github.com/treangenlab/emu