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Hello,
I was applying your pipeline to some sc-data from the allen brain atlas and i got a handful of negative values for the 3'UTR length in my sce object. I was using the utrome_mm10_v2. One exam…
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### Description
I installed `outrigger` using the `environment.yml` file and didn't get the command line entry points, so I installed via `pip` and then got errors with the C libraries of `pysam`.
…
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```javascript
TypeError: Cannot read properties of undefined (reading 'element')
at b.element in src/vs/base/browser/ui/list/listView.ts:780:28
at in src/vs/base/browser/ui/list/listWidget.ts:244:98
…
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Hi, thanks for developing and maintaining such an excellent tool.
I am trying to use TensorQTL to analyze some methylation data. I'm thinking of taking a similar strategy as eQTL and sQTL, where a …
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Dear Alex,
I encountered an error during the process of building my reference.
The two files for input are as follows, which are sourced from [RefSeq FTP sites](https://ftp.ncbi.nlm.nih.gov/geno…
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Hi,
I am trying to use loftee plugin (Grch38) as a part of VEP and I got the following error.
Could you please help?
Thanks in advance
**Command used**
docker run -t -i -v /home/vep_data/:/…
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Hi there,
I'm trying to run omark on a few annotations with `omark -f ${species}.omamer -d /.../LUCA-v2.0.0.h5 -o output -i ${species}.splice`. I ran omamer before with `omamer search --db /.../LUC…
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For minimap2 (versions 2.25 and above), it seems like the miniprot splice model is used for aligning RNA-seq reads by default. According to the miniprot paper, there are fixed penalty scores associate…
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I test one example read (`CTGGCTGGAGCAGCGGGACCGCTCCATCCGAGAGAAGCAGAGTGATGATGAGGTTTATGCGCCAGGT`), and run STAR with `--alignSJDBoverhangMin 1` argument.
The last 3rd base *..TATGCGCCA***G** is the …
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Hi! I'm trying to get the annotation files using hg38 Ensembl GTF file.
I'm running it this way:
`python3 create_annotator.py -g Homo_sapiens.GRCh38.97.gtf -a hg38_ensembl`
And I'm getting t…