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### Checklist
- [X] I added a descriptive title
- [X] I searched for other issues and couldn't find a solution or duplication
- [X] I already searched in Google and didn't find any good informati…
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**1. What were you trying to do?**
Compare number of reads mapped from `vg mpmap` with number of reads mapped with `kallisto`.
**2. What did you want to happen?**
Know what is the number of "…
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I'm not sure what format old Stringtie used, but Stringtie2 outputs a gtf file containing both the transcript locations and the quantities.
When I try the method suggested in the vignette, using i…
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**Are you using the latest release?**
Currently in 1.8.11
**Describe the bug**
`funannotate annotate` doesn't parse the COG annotations into the gbk file output if the input is a gbk file, but it…
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Hi rna-seq-pop developper,
I am having problem installing this pipeline using conda:
`ls`
**_config LICENSE README.md resources RNA-Seq-Pop-Logo.png workflow_**
`snakemake --use-conda -…
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I have a feature request and some discussion around the pbspro executor and how resource settings are determined from `cpus`, `memory`, and `clusterOptions`.
So we have a pipeline with the standard…
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Hello,
I recently updated the indexes I am using for kallisto from version 93 to 96. I tried to create genomebam files and I used the same chromosome file I was using in the past. However, now I am…
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Hi,
Thanks for developing this powerful tool. But when I processed the BAM file from the CellRanger pipeline with bamtofastq, the results didn't match the original FASTQ sequencing data. The code is …
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**Describe the issue**
`kb info` returns a non-zero exit status, which is unexpected since no errors occurred and no undefined syntax was used.
**What is the exact command that was run?**
```
…
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Mapping rate should be obtainable from a kallisto output file, so `updated_metadata` is no longer necessary as we discussed a long time ago. @Hego-CCTB Could you work on that? It would be great if you…