search

motu-tool / mOTUs

motus - a tool for marker gene-based OTU (mOTU) profiling
GNU General Public License v3.0
144 stars 24 forks source link

no unassigned with full taxonomy #89

Closed gitcat01 closed 2 years ago

gitcat01 commented 2 years ago

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!

AlessioMilanese commented 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