NGLess

Dear Luis, not directly related to ngless, but the ngless contributions: a metaphlan update to

This is an idea that goes back to the early days of NGLess and Paulo Monteiro even implemented

Hi List, NGLess version 1.4.0 has been released. This is less about big changes and more that a lot

While testing the beta, I fixed a few more bugs and am releasing it as v1.4.0-beta2 https://github.

If anyone else is ever running into this sam/bam issue, it seems to be related to https://github.com/

You can use discard_zeros=True in the count() call https://ngless.embl.de/Functions.html#count HTH

Just a quick update - I tried running the script with the "--subsample" flag just to ensure

Currently, no; but this is not a bad idea for a future version. Best Luis Luis Pedro Coelho | Fudan

I would guess that it's not so much about the size of the initial read, but whether you can

There is currently no simple way to do this in NGLess (although another person asked me about it this

Dear Jane, I believe that the issue here is that by changing the version declaration line in your

I was also not aware of motus 3 until your email :) I think this does go on our TODO list, though

Dear Yu-Jen, (Sorry for the delay in replying, this was a busy week). The way to approach this within

On 7/8/21 11:10 AM, Xianghui Liu wrote: > I want to ask, motu can run by itself vs run by ngless,

Demand has indeed outstripped supply, so I posted a second date: July 5 https://forms.gle/

But in my case, it's the other way around. The dist1 file is much bigger than all1. Any

Dear Vadim, In principle, yes, the functions should only read fastq files. I would expect that most

That is strange. Are the script.ngl files in those directories the same? Best Luis Luis Pedro Coelho

Hi Ulrike, There currently is not, but feel free to open an issue about it (as a feature request) as

The modules evolve somewhat separately from the main programme, so there has been no update to them

Hi Ulrike, (Because of the Lunar New Year celebrations, I'm now catching up with a lot of the non

Dear Luis: The example scripts you provided used 'scaled'. However, I am trying to do use

I would guess counts = count(mapped, map_file="prok-OM-RGC-v2.0.0.emapper.annotations-v2.tsv.xz

Dear List, As discussed before, we've released NGLess 1.3.0, which contains a series of small

Oh, this is a very good point. The checks for headers are indeed not run on --validate-only (although

I just committed a slight improvement so that you'd get a much better error message in the future

When you think about it, I don't it make sense first to sum all the reads mapping to genes with a

Ah, ok. I read your previous message too fast. I tested it locally and, indeed, they behave

Hi all, I'm working with NGLess to annotate a couple of marine metagenomes samples. I was

Hi Queten, I recently joined this group, and I read your question so I hope that my answer don't