How to use NGLess to generate gene count matrix?

[Yu-Jen Chang]

I used your tool NGLess to generate count table by using your human-gut.ngl profiler, but the output is doesn't meet my need.

I want to generate a tab-separated values matrix giving the number of reads mapped on genes (rows) across metagenomic samples (columns). 

I am not familiar with metagenomic WGS pipeline, so I really need your help !!

Thank you!

All the best,

Yu-Jen

[Luis Pedro Coelho]

Dear Yu-Jen,

(Sorry for the delay in replying, this was a busy week).

The way to approach this within NGLess is to use the parallel module:

https://ngless.embl.de/stdlib.html#parallel-module

Also, do note that the motus version from that script is now a bit outdated. Because of a desire to keep backwards compat, I have hesitated a bit too long to update the ng-meta-profiler repository, but I just did so

https://github.com/ngless-toolkit/ng-meta-profiler/blob/master/human-gut-profiler.ngl

HTH,

Luis

Luis Pedro Coelho | Fudan University | http://luispedro.org

https://orcid.org/0000-0002-9280-7885

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