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Luis Pedro Coelho
,
ullo...@googlemail.com
2
Jun 6
NGLess 1.5 Ideas
Dear Luis, not directly related to ngless, but the ngless contributions: a metaphlan update to
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NGLess 1.5 Ideas
Dear Luis, not directly related to ngless, but the ngless contributions: a metaphlan update to
Jun 6
Luis Pedro Coelho
Jun 1
NGLess Script Builder
This is an idea that goes back to the early days of NGLess and Paulo Monteiro even implemented
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NGLess Script Builder
This is an idea that goes back to the early days of NGLess and Paulo Monteiro even implemented
Jun 1
Luis Pedro Coelho
Jun 1
NGLess Version 1.4.0
Hi List, NGLess version 1.4.0 has been released. This is less about big changes and more that a lot
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NGLess Version 1.4.0
Hi List, NGLess version 1.4.0 has been released. This is less about big changes and more that a lot
Jun 1
Luis Pedro Coelho
3
May 26
NGLess Version 1.4.0 beta
While testing the beta, I fixed a few more bugs and am releasing it as v1.4.0-beta2 https://github.
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NGLess Version 1.4.0 beta
While testing the beta, I fixed a few more bugs and am releasing it as v1.4.0-beta2 https://github.
May 26
ullo...@googlemail.com
2
May 13
GMGC split pipeline
If anyone else is ever running into this sam/bam issue, it seems to be related to https://github.com/
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GMGC split pipeline
If anyone else is ever running into this sam/bam issue, it seems to be related to https://github.com/
May 13
ullo...@googlemail.com
,
Luis Pedro Coelho
2
Mar 17
option to not report zero abundance genes count + collect
You can use discard_zeros=True in the count() call https://ngless.embl.de/Functions.html#count HTH
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option to not report zero abundance genes count + collect
You can use discard_zeros=True in the count() call https://ngless.embl.de/Functions.html#count HTH
Mar 17
Alyse Larkin
,
Luis Pedro Coelho
5
Feb 17
GMGC marine database indexing runs out of memory
Just a quick update - I tried running the script with the "--subsample" flag just to ensure
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GMGC marine database indexing runs out of memory
Just a quick update - I tried running the script with the "--subsample" flag just to ensure
Feb 17
ullo...@googlemail.com
,
Luis Pedro Coelho
2
Feb 16
ngl string replace
Currently, no; but this is not a bad idea for a future version. Best Luis Luis Pedro Coelho | Fudan
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ngl string replace
Currently, no; but this is not a bad idea for a future version. Best Luis Luis Pedro Coelho | Fudan
Feb 16
ullo...@googlemail.com
,
Luis Pedro Coelho
2
Jan 24
Thresholds for gene catalog mapping
I would guess that it's not so much about the size of the initial read, but whether you can
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Thresholds for gene catalog mapping
I would guess that it's not so much about the size of the initial read, but whether you can
Jan 24
ullo...@googlemail.com
,
Luis Pedro Coelho
5
11/25/21
Mixed paired end and single end reads
There is currently no simple way to do this in NGLess (although another person asked me about it this
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Mixed paired end and single end reads
There is currently no simple way to do this in NGLess (although another person asked me about it this
11/25/21
Jane
,
Luis Pedro Coelho
2
11/22/21
collect() not working
Dear Jane, I believe that the issue here is that by changing the version declaration line in your
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collect() not working
Dear Jane, I believe that the issue here is that by changing the version declaration line in your
11/22/21
Yu-Jen Chang
, …
Luis Pedro Coelho
5
10/22/21
motus version issues
I was also not aware of motus 3 until your email :) I think this does go on our TODO list, though
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motus version issues
I was also not aware of motus 3 until your email :) I think this does go on our TODO list, though
10/22/21
Yu-Jen Chang
,
Luis Pedro Coelho
2
10/1/21
How to use NGLess to generate gene count matrix?
Dear Yu-Jen, (Sorry for the delay in replying, this was a busy week). The way to approach this within
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How to use NGLess to generate gene count matrix?
Dear Yu-Jen, (Sorry for the delay in replying, this was a busy week). The way to approach this within
10/1/21
mette Joergensen
, …
Renato Alves
12
7/8/21
Problem with mOTU version 2.5 and genus counts
On 7/8/21 11:10 AM, Xianghui Liu wrote: > I want to ask, motu can run by itself vs run by ngless,
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Problem with mOTU version 2.5 and genus counts
On 7/8/21 11:10 AM, Xianghui Liu wrote: > I want to ask, motu can run by itself vs run by ngless,
7/8/21
Luis Pedro Coelho
2
6/9/21
NGLess Tutorial
Demand has indeed outstripped supply, so I posted a second date: July 5 https://forms.gle/
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NGLess Tutorial
Demand has indeed outstripped supply, so I posted a second date: July 5 https://forms.gle/
6/9/21
ullo...@googlemail.com
,
Luis Pedro Coelho
6
4/22/21
counting in ngless dist1/all1
But in my case, it's the other way around. The dist1 file is much bigger than all1. Any
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counting in ngless dist1/all1
But in my case, it's the other way around. The dist1 file is much bigger than all1. Any
4/22/21
Vadim Puller
,
Luis Pedro Coelho
2
3/11/21
Reading fasta files (rather than fastq): "Number of lines in FastQ file is not multiple of 4! EOF found"
Dear Vadim, In principle, yes, the functions should only read fastq files. I would expect that most
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Reading fasta files (rather than fastq): "Number of lines in FastQ file is not multiple of 4! EOF found"
Dear Vadim, In principle, yes, the functions should only read fastq files. I would expect that most
3/11/21
Ulrike Löber
,
Luis Pedro Coelho
4
3/5/21
interrupted ngless run lock1
That is strange. Are the script.ngl files in those directories the same? Best Luis Luis Pedro Coelho
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interrupted ngless run lock1
That is strange. Are the script.ngl files in those directories the same? Best Luis Luis Pedro Coelho
3/5/21
ullo...@googlemail.com
,
Luis Pedro Coelho
2
3/2/21
paired fastq recognize different pattern
Hi Ulrike, There currently is not, but feel free to open an issue about it (as a feature request) as
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paired fastq recognize different pattern
Hi Ulrike, There currently is not, but feel free to open an issue about it (as a feature request) as
3/2/21
Erwin Sentausa
, …
Luis Pedro Coelho
6
3/1/21
IGC module annotated using eggNOG mapper v2
The modules evolve somewhat separately from the main programme, so there has been no update to them
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IGC module annotated using eggNOG mapper v2
The modules evolve somewhat separately from the main programme, so there has been no update to them
3/1/21
ullo...@googlemail.com
,
Luis Pedro Coelho
2
2/21/21
Mouse metagenome using GMGC or MouseGutCatalog
Hi Ulrike, (Because of the Lunar New Year celebrations, I'm now catching up with a lot of the non
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Mouse metagenome using GMGC or MouseGutCatalog
Hi Ulrike, (Because of the Lunar New Year celebrations, I'm now catching up with a lot of the non
2/21/21
Xianghui Liu
2/17/21
How to do normalization?
Dear Luis: The example scripts you provided used 'scaled'. However, I am trying to do use
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How to do normalization?
Dear Luis: The example scripts you provided used 'scaled'. However, I am trying to do use
2/17/21
Rémy Dugauquier
, …
ullo...@googlemail.com
6
2/9/21
Adapt processing shotgun metagenomes
I would guess counts = count(mapped, map_file="prok-OM-RGC-v2.0.0.emapper.annotations-v2.tsv.xz
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Adapt processing shotgun metagenomes
I would guess counts = count(mapped, map_file="prok-OM-RGC-v2.0.0.emapper.annotations-v2.tsv.xz
2/9/21
Luis Pedro Coelho
2/5/21
ANN: NGLess 1.3.0
Dear List, As discussed before, we've released NGLess 1.3.0, which contains a series of small
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ANN: NGLess 1.3.0
Dear List, As discussed before, we've released NGLess 1.3.0, which contains a series of small
2/5/21
Luis Pedro Coelho
, …
Ulrike Löber
6
1/25/21
Preparing NGLess 1.3
Oh, this is a very good point. The checks for headers are indeed not run on --validate-only (although
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Preparing NGLess 1.3
Oh, this is a very good point. The checks for headers are indeed not run on --validate-only (although
1/25/21
ullo...@googlemail.com
,
Luis Pedro Coelho
4
1/22/21
sorted BAM output
I just committed a slight improvement so that you'd get a much better error message in the future
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sorted BAM output
I just committed a slight improvement so that you'd get a much better error message in the future
1/22/21
mette Joergensen
,
Luis Pedro Coelho
5
1/21/21
Normalization of counts
When you think about it, I don't it make sense first to sum all the reads mapping to genes with a
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Normalization of counts
When you think about it, I don't it make sense first to sum all the reads mapping to genes with a
1/21/21
Vadim Puller
,
Luis Pedro Coelho
6
1/19/21
NGLess counting of paired reads
Ah, ok. I read your previous message too fast. I tested it locally and, indeed, they behave
unread,
NGLess counting of paired reads
Ah, ok. I read your previous message too fast. I tested it locally and, indeed, they behave
1/19/21
Christian Hodar
1/4/21
Question about VFDB
Hi all, I'm working with NGLess to annotate a couple of marine metagenomes samples. I was
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Question about VFDB
Hi all, I'm working with NGLess to annotate a couple of marine metagenomes samples. I was
1/4/21
Quinten Ducarmon
, …
Christian Hodar
19
1/4/21
Taxonomic/functional annotations and interpretation of read abundance
Hi Queten, I recently joined this group, and I read your question so I hope that my answer don't
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Taxonomic/functional annotations and interpretation of read abundance
Hi Queten, I recently joined this group, and I read your question so I hope that my answer don't
1/4/21