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Dear Professor
I am writing to request access to the bbmap/repair.sh script . I am currently engaged in a project where I need to convert .mate1 and .mate2 files generated by STAR into 1.fastq.gz an…
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fastq-to-ubam naming convention for output:
```
/${sample}/HAS_READ_GROUP/{readGroup}/HAS_FASTQ/${jobRequestId}_${sample}_${readGroup}.ubam
```
1000 Genomes Fastq name:
```
ERR3239279_1.fastq.gz
``…
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When passing the `--rightfq` and `--leftfq` args, the `$ensure_full_path method` is only effectively called on the first file in the list of fastq files (`ensure_full_path` doesn't support lists of fi…
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Dear developers,
we installed MIRA on our Ubuntu server, which we access remotely, "docker compose up -d" starts the docker correctly, as we can see from "docker ps". The only change we made in the…
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Hi I installed zarp-cli when when ran on the paired-end fastq files, it initialized but then got the error on htsinfer.
Input command
`zarp ER14_1.fastq,ER14_2.fastq`
output error is attached:
…
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Hey there,
First, just wanna say thanks for this truly iconic pipeline, it has made analysing my DMS data a total breeze.
But the reason I'm posting is I'm trying to understand exactly what is g…
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I apologize for such a question, but should we use all the generated FASTQ files (including failed ones to merge) for the alignment? Or do you suggest using only the successfully merged fastq files?
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Hii Robert
I have a new MacBook Pro with following specifications
Chip Apple M3 Max
Memory 36GB
macOS Sonoma 14.1
I was trying to test the Bactopia using docker…
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In the previous version of the pipeline, there were options in the config file for limiting the cpus and memory usage, but these parameters seem to be gone. In run.nf, I see how we can set params for…
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I'm trying to run HiC-Pro on a test data of my own, but After setting all the parameters i get the strange error, that my files are not found. But somehow it searches for the wrong files.
This is …