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1. Minimum core metadata attributes for search. There was a spreadsheet with a minimal set that was circulated on the discovery side which I can’t find again. I *think* it may have been from Tony Bro…
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I see that transcripts have the method to get sequences while the gene class does not. Would be nice to be able to get genomic DNA of gene as well.
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Hello, I have several questions.
Q1: In your custom human library, miRNAs of SNPs are represented and merged together (after alignment and counting). How did you decide on which SNPs to represent?…
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Thank you for taking the time to contribute an issue!
**Describe the bug**
File "scout/scout/load/setup.py", line 164, in setup_scout
ensembl_id = gene_obj["ensembl_id"]
…
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Based on this discussion: https://github.com/HGVSnomenclature/hgvs-nomenclature/discussions/49.
As the r. coordinate type refers to mature (coding) RNA molecules, descriptions using the r. coordina…
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I am using GRCH38 as ref genome, and would like to create GC correction and RT files based on my own data (did not use GRCH38 ref loci or alleles files available). I have successfully created GC corre…
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The attached file does not sort properly by chromosome start and stop:
[tf_locus.bed.gz](https://github.com/biocore-ntnu/pyranges/files/7018207/tf_locus.bed.gz)
```
>>> import pyranges
>>> dat…
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As seen in proposed usage patterns in the upcoming G2P endpoints (https://github.com/ohsu-computational-biology/schemas/blob/apichanges/doc/source/api/proposed_schema_changes.md) as well as the pendin…
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The VCFs generated by QDNAseq do not conform to the specification for the reference allele field, as they contain symbolic alleles e.g. ``. This results in errors when trying to either validate the VC…
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**ISSUE**
First of all, I found DeepVariant to be a very good and innovative tool. I'm considering including it in my exome analysis pipeline. I followed the tutorial (DeepVariant worked correctly wi…