How to use NGLess to generate gene count matrix?

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Yu-Jen Chang

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Sep 28, 2021, 1:12:18 AM9/28/21
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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.
螢幕擷取畫面 2021-09-28 105752.png
I want to generate a tab-separated values matrix giving the number of reads mapped on genes (rows) across metagenomic samples (columns). 
螢幕擷取畫面 2021-09-28 112259.png
I am not familiar with metagenomic WGS pipeline, so I really need your help !!
Thank you!

All the best,
Yu-Jen

Luis Pedro Coelho

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Oct 1, 2021, 5:04:18 AM10/1/21
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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:


Also, do note that the motus version from that script is now a bit outdated.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


HTH,
Luis


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