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Hi,
I am using the newest version 0.0.2 isONclust3 and would like to try the `--gff` flag and see what is the different between the default and with the `--gff` flag
here is my command
```
a…
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~ Hi, it's my first time here. I'm trying to run Snippy for the first time with the following script:
snippy-multi ../pwd_assembly --ref ../sequence.fasta --outdir snippy_analise --cpus 16
~ But…
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Hi @Zhiliang-Bai ,
Thanks for your code.
I am wondering how to generate `RV=$tmp/${sample}_R1_filtered.final.fastq.gz` from raw reads before running `st_pipeline_run.py`. Trimming read 1 with …
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### Discussed in https://github.com/bio-raum/FooDMe2/discussions/76
Originally posted by **gregdenay** November 22, 2024
Hi @marchoeppner
some colleagues that are actively working on metho…
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Hello there,
I am posting this issue beacuse after running atlas qc on my samples, I find a new folder called Intermediate, that contains qc, which in turn contains decontamination. Inside decontam…
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I have a large list of fastq files that will be used for the same database.
Is there a simple way to run the command on a list of files for the same Meryl database or do I need to concatenate all o…
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Hello, any suggestions to perform a _de novo_ assembly of Meccus pallidipennis and how to generate the corresponding config file? Considering that I have a fastq.qz file with 5.93 million unphased rea…
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### Description of feature
The samplesheet of ampliseq looks different to the other nf-core pipelines. I would propose the standardization of the headers of the samplesheet in ampliseq for:
- [ ] sa…
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ForkPoolWorker-2: [====________________] 22% (9.3GB/40.7GB) ForkPoolWorker-2: [09:06:18] Error accessing 'https://d.pcs.baidu.com/rest/2.0/pcs/file'
ForkPoolWorker-2: [09:06:18] Function: _downchu…
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seem to have isolated it to this step:
minimap2 -a -t 2 -R "@RG\tID:run1\tSM:sample1\tLB:library1\tPL:ILLUMINA" refs/AF086833.fa reads/SRR1553425_1.fastq reads/SRR1553425_2.fastq | \
> samtools so…