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Hello!
I have been having an issue running umi_tools dedup. I'm using umi-tools version 1.1.0.
I aligned my paired-end reads using STAR, converted the sam files to bam, sorted and indexed and t…
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Dear sir,
I met problem in step10
Mapping with Bowtie2 (Langmead and Salzberg 2012, Nat Methods 9(4), 357-9)
Creating reference from contigs
Working with sample 1: A7
Getting raw reads
…
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Hi,
Thanks for the useful tool. Would it be possible to add the option to modify the headers of the output fastq files? I can see in `aligner.py` that the (final) command for generating clean reads…
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I was running midas as a module,
module load midas /1.3.2
I encountered this error
Error: could not execute samtools binary: samtools
(exited with error code 127)
To solve this issue, follow the…
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It might be worthwhile to add samtools to the installation requirements list. I used the suggested command:
```
conda install numpy scipy cython numba matplotlib scikit-learn h5py click
```
Then I…
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### Ask away!
I'm using this workflow on our HPC via Singularity. The input bam is a Promethion run mini bams merged via samtools merge into a single bam (140GB). Is this a missing header issue or a …
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My circlator (Circlator version: 1.5.5) run with the following command was running for 3 days and then stopped and never continued. Here is the last part of the log file:
Command:
```
circlator a…
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Hi
using the "gem install" command I get the following error:
> Fetching bio-polyploid-tools-1.2.1.gem
Fetching systemu-2.6.5.gem
Fetching descriptive_statistics-2.5.1.gem
Fetching bi…
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Hi all, I am working on benchmarking variant calling tools and I am now simulating low and high coverage hifi reads for this purpose. But I am not sure whether my workflow is correct as I received mes…
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Consider using the automated tool to facilitate this https://nf-co.re/docs/contributing/modules#migrating-from-pytest-to-nf-test
### Is your feature request related to a problem? Please describe
…