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I followed the STARTbio tutorial and when I tried to perform the Bowtie index of the genome (https://artbio.github.io/startbio/AnalyseGenomes_2023/Preparing_reference/#2-index-dmel-r654-for-bowtie), I…
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### What Docs changes are you proposing?
Write a guide that teaches implementers how to use [Bowtie](https://docs.bowtie.report/en/stable/) to test schemas across validator implementations.
### Code…
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Hey,
I have an issue to start your pipeline, since it skipps the first steps and starts directly with feature counts which of course won't work. I tried to start the cutadapt task manually, which a…
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![2024-10-28_00 39 07](https://github.com/user-attachments/assets/4c1381b6-a80d-44b6-970c-29cfe…
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Hello,
Thank you for the tool, I am excited to put it to use. I successfully ran the test and it completed. On real data however, I get an error. My sRNA data was originally in fastq, so I converte…
SamCT updated
5 months ago
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### Description of the bug
When I run nf-core/mag with the
```
--host_fasta_bowtie2index "/path/to/references/"
```
The bowtie log file gives me the following warning
```
Warning: Output file './…
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When and index has been specified in the config file (i.e. `metaphlan_index_name: mpa_vOct22_CHOCOPhlAnSGB_202212`) and those files for that version are already installed in the in the metabphlan_bd d…
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Dear developers,
I am currently working with miRNA-seq reads from Illumina platforms, whose length ranges roughly from 16 to 30 nucleotides.
Do you think bowtie can outperform other popular mapp…
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I have these in the same folder as the path for the genome fa = hg19.fa
However, this does not detect the ebwt files and constantly builds the index using bowtie build.
Is there anything wrong in the…
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```
...BOWTIE PE is still running ..from one week! No errors, seems that there are
no progress in the output stream. I attach it. The input reads are the same I
used for the other modules: did you h…