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ullo...@googlemail.com
,
Luis Pedro Coelho
4
10/6/23
YAML input count & collect
Sorry that was way too quick I think the answer is that you leave them out: collect(count, ofile=
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YAML input count & collect
Sorry that was way too quick I think the answer is that you leave them out: collect(count, ofile=
10/6/23
Jane
9/3/23
Taxonomic and functional annotation together
Dear Luis, I've been using NGLess for a while but only recently discovered this Google Groups - I
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Taxonomic and functional annotation together
Dear Luis, I've been using NGLess for a while but only recently discovered this Google Groups - I
9/3/23
Victor Hugo Jarquín
8/18/23
Logic error in StandardModules/parallel
Dear NGLess group, I am running the pipeline for taxonomic annotation. However, I am getting the
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Logic error in StandardModules/parallel
Dear NGLess group, I am running the pipeline for taxonomic annotation. However, I am getting the
8/18/23
Ro Bert
,
Renato Alves
2
8/8/23
memory usage of bwa mem
Hi Robert, The block_size_megabases and the -K option are related in purpose but do different things.
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memory usage of bwa mem
Hi Robert, The block_size_megabases and the -K option are related in purpose but do different things.
8/8/23
Luis Pedro Coelho
,
juli...@free.fr
2
7/17/23
ANN: NGLess v1.5.0
Hi luis, do you have an example of script that combine yaml, paired read and motus? I tried something
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ANN: NGLess v1.5.0
Hi luis, do you have an example of script that combine yaml, paired read and motus? I tried something
7/17/23
Luis Pedro Coelho
2/17/23
NGLess video tutorials
Hi everyone, Maybe people on this list do not need the tutorials as it's covering the very basics
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NGLess video tutorials
Hi everyone, Maybe people on this list do not need the tutorials as it's covering the very basics
2/17/23
ullo...@googlemail.com
1/24/23
High memory consumption mapping GMGC
Dear all, did anyone ever observe an unusually high memory consumption performing the mapping within
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High memory consumption mapping GMGC
Dear all, did anyone ever observe an unusually high memory consumption performing the mapping within
1/24/23
mette Joergensen
,
Luis Pedro Coelho
4
1/9/23
Problem with installation
Hi Mette, A few possible solutions: 1 (easiest, probably slow). Just install the following binary
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Problem with installation
Hi Mette, A few possible solutions: 1 (easiest, probably slow). Just install the following binary
1/9/23
Josh Sekela
,
Luis Pedro Coelho
4
11/14/22
Writing a mapped readset to fastq - only 1 file written?
Unfortunately, this is not possible atm, but I agree that this would be a good setting to have and I
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Writing a mapped readset to fastq - only 1 file written?
Unfortunately, this is not possible atm, but I agree that this would be a good setting to have and I
11/14/22
mette Joergensen
, …
ullo...@googlemail.com
13
10/22/22
Problem with mOTU version 2.5 and genus counts
Hi Luis, hi Renato, I have tried to setup mOTUs v3 recently following the instructions on https://
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Problem with mOTU version 2.5 and genus counts
Hi Luis, hi Renato, I have tried to setup mOTUs v3 recently following the instructions on https://
10/22/22
Josh Sekela
,
Luis Pedro Coelho
6
7/21/22
NGLess -> featureCounts?
Much appreciated, I just updated our Conda install. On Tuesday, July 19, 2022 at 8:27:20 PM UTC-4 lu.
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NGLess -> featureCounts?
Much appreciated, I just updated our Conda install. On Tuesday, July 19, 2022 at 8:27:20 PM UTC-4 lu.
7/21/22
Luis Pedro Coelho
7/21/22
ANN: NGLess v1.4.2
Dear List, As previously discussed here, I just released v1.4.2 with a bugfix for parsing of GFF
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ANN: NGLess v1.4.2
Dear List, As previously discussed here, I just released v1.4.2 with a bugfix for parsing of GFF
7/21/22
Luis Pedro Coelho
2
7/18/22
Specifying samples with YAML in NGLess
The YAML file can contain multiple samples and will also work well with parallel ngless "1.5
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Specifying samples with YAML in NGLess
The YAML file can contain multiple samples and will also work well with parallel ngless "1.5
7/18/22
Luis Pedro Coelho
,
ullo...@googlemail.com
2
6/6/22
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
6/6/22
Luis Pedro Coelho
6/1/22
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
6/1/22
Luis Pedro Coelho
6/1/22
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
6/1/22
Luis Pedro Coelho
3
5/26/22
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.
5/26/22
ullo...@googlemail.com
2
5/13/22
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/
5/13/22
ullo...@googlemail.com
,
Luis Pedro Coelho
2
3/17/22
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
3/17/22
Alyse Larkin
,
Luis Pedro Coelho
5
2/17/22
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
2/17/22
ullo...@googlemail.com
,
Luis Pedro Coelho
2
2/16/22
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
2/16/22
ullo...@googlemail.com
,
Luis Pedro Coelho
2
1/24/22
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
1/24/22
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
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