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jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
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antimicrobial function SQMlite #851

Open inej90 opened 3 weeks ago

inej90 commented 3 weeks ago

Dear Fernando,

I load my project with loadSQMlite (combination long reads project). Then, I was trying to get the abundance of antimicrobial function (top ten) and plot it but I always obtain the message: at least one of you items is not in the rows. I know that with SQMlite, I cannot use subset. What can I use in this case?

NB: I am working on KEGG.

Thank you very much in advance.

fpusan commented 3 weeks ago

If this project was obtained using sqm_longreads.pl then the filtering can be done at the sqmreads2tables.py step. Check the PDF manual. If this is a normal SqueezeMeta.pl run you will need to load the whole project (not only the tables ) in SQMtools and do it from there.