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Recent Replies
Comment: How to map and annotate gene symbols to gene type?
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GenoMax
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Yes it should. Look for `biotypes` ([LINK][1]).
[1]: https://www.ensembl.org/info/genome/genebuild/biotypes.html
Comment: How to map and annotate gene symbols to gene type?
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mohammedtoufiq91
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@genomax thank you. Does this works in `biomart` R package too?
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Use BioMart at [**Ensembl**][1]. Choose `Attributes` as needed.
![enter image description here][2]
[1]: http://www.ensembl.org/in…
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`makeblastdb` is creating the index from `mydb.fsa` (which is your reference) file. This results in the set of files you name above. `mydb`…
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Try [brename](https://github.com/shenwei356/brename), it's safe and powerful. also read this post: https://www.biostars.org/p/9487877/
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The `brename` version should be
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I think the issue is that the `seqlevels `do not match. Apparently, one should be a subset of the other. You could try restricting only to …
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I do not know how you want to downsample vcf file,. However, to downsample reads, you can use `seqtk sample` https://github.com/lh3/seqtk …
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I would also recommend checking out a different star allele-calling tool named PyPGx (see [docs](https://pypgx.readthedocs.io/en/latest/rea…
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I prefer the `rename` tool. I think you might need to install it with either something like `apt` (ubuntu), or `conda` (Linux, Mac, Windows…
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If I'm interpreting you correctly, you want to compare the VCF files, ignore SNPs shared by two (or more) species, and instead retain only …
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Thank you I realized that the mistake I made was by not making a docker image.
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Which ID and QUAL values do you pick for the output VCF record? That choice makes the difference.
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> I've queried the Panther database, but unfortunately it does not return annotations for all of my genes.
For any reasonably-sized quer…
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