Closed gitcat01 closed 2 years ago
Hi,
I was using mOTU on marine metagenomes and it works great!
Nice to hear!
However, I used flags -A -c to report counts and full taxonomy but then I don't receive number of unassigned reads.
Unfortunately the output format with -A
is designed not to have unassigned
. You need to run mOTUs two times to find this information. The first time you run it, you can save the intermediate MGC count with -M
so that the second run is much faster. For example:
motus profile -s db_mOTU/db_mOTU_test/test1_single.fastq -A -c -M temp.mgc > res_temp
motus profile -c -m temp.mgc | grep -P "unassigned\t" > res_temp2
cat res_temp res_temp2 > RESULT
Hi,
I was using mOTU on marine metagenomes and it works great! However, I used flags -A -c to report counts and full taxonomy but then I don't receive number of unassigned reads. Is there a way to receive counts, full taxonomy and unassigned reads?
Thank you very much!