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We can currently `count()` reads overlapping with regions defined in a GFF file.
However this is only accessible for counting.
Another use-case is within `select()` in order to keep/drop reads tha…
unode updated
5 years ago
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When working with very large SAM files it is often convenient to remove sequence and quality information to reduce storage and improve I/O.
Following from this it would be convenient to have a `str…
unode updated
4 years ago
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what does CLP and CDP mean in the results? There is no information on them, I just checked using chatgpt, it said that CLP (Classical Lipopeptides) and CDP (Cyclic Depsipeptides). I don't know if it …
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I encountered an error while running the abundance subcommand:
macrel abundance -1 SRR16178793_1.fastq.gz -2 SRR16178793_2.fastq.gz --fasta peptide.fasta --output ./output/SRR16178793_abun --tag ./ou…
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This error occurs when using `map()` together with `minimap2` and saving as a `.bam`.
```
import "minimap2" version "1.0"
...
minimap_mapped = map(input, fafile=REFDB, mode_all=True, mapper="min…
unode updated
4 years ago
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Hi,
I am running the pipeline in an slurm enviroment and even though I specified the `-t` to write into scratch, the pipeline start to write on `~/.local/share/ngless` (specifically /users/valensan/.…
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Hi,
I seems if I had a job running IGC mapping, and while it is underway I start another job running IGC mapping, I will receive the broken pipe error.
```
[Wed 18-09-2019 10:58:47] Line 15: St…
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Hello,
Thank you for developing metaSNV!
I'd like to try it with bam files I obtained by aligning metagenomics reads to a custom reference using bwa-mem. Following metaSNV userguide, I'm trying t…
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Hi
Although the igc module has been bump to 1.0, but module.yaml (also Makefile) still says version 0.9.0, hence ngless is expecting 0.9.0 instead.
```
ngless/Modules/igc.ngm/1.0/module.yaml
…
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Since ngless 0.10.0 index files created by bwa are versioned `reference.fa-bwa-0.7.17.gz.bwt` instead of `reference.fa.gz.bwt`.
The bundled reference genomes (`hg19`, `mm10.p5`, ...) include `bwa` …
unode updated
2 years ago