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### Description of the bug
Running CellRanger with all GEX samples, in which there are multiple barcodes per sample, but the all go to the same sample (see the samples & barcodes tables below).
Thi…
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I've experienced a memory leak when using the python `mappy.Aligner` when initialized with a sequence file/FASTA (this is within [Megalodon](https://github.com/nanoporetech/megalodon)). This same memo…
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Hi
I am running the variant calling pipeline with vardict and mutect2..After calling variants and during the annotation process I get this error -
```
[2022-02-09T12:12Z] Calculating variation …
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When I run **BAMboozle 0.5.0** on BAM files generated with **Salmon 1.6.0**, I get the following error message:
```
BAMboozle --bam sample01.bam --out sample01.anonym.bam --fa /mnt/data/reference_…
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See https://github.com/brewsci/homebrew-bio/search?q=%22needs+openmp%22
| Formula | PR | Merged? |
| :--- | :---: | :---: |
| `arcs` | | |
| `arks` | | |
| `biobloomtools` | | |
| `bracken` | …
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This is related to #232 I was getting on my laptop - the `"Bio.Alphabet has been removed from Biopython` error. You had suggested trying version `2.2.8` so I'm pulling the latest master from github to…
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```
Hello,
I'm getting a segmentation fault while trying to align reads to a bacterial
genome. I was able to isolate the problem to the following read:
@M01793:3:000000000-A5GLB:1:1101:14294:3045 1…
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There's no documentation I can find about how kallisto handles mismatches to the reference transcriptome. Is there any way to set a maximum value or to quantify the mismatches, such as for the purpose…
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Dear all,
I would like to know if there is a way to properly visualize methylation information obtained from modkit in IGV genome browser (testing IGV 2.17 snapshot).
In particular, I ran Dorado wit…
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**Version info**
- bcbio version (bcbio_nextgen.py --version): 1.2.2
- OS name and version: Ubuntu 18.04.4 LTS
**To Reproduce**
- Exact bcbio command you have used
/usr/local/bcbio/anaconda/…