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Gene set tracks are returning ENS not gene_name #113

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DLBPointon opened this issue Jun 13, 2023 · 2 comments
Open

Gene set tracks are returning ENS not gene_name #113

DLBPointon opened this issue Jun 13, 2023 · 2 comments
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bug Something isn't working Release 2 Issues related to the TreeVal 2.0
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@DLBPointon
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Description of the bug

A large number of the gene set annotations used on treeval are using the ENS number rather than the more desired gene name.

This would be more helpful and stop any uneccessary extra work to find what finds are.

also remove chromosome id from this, why are they even there?

Script needs rewriting, genesets re-downloaded and re-parsed.

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@DLBPointon DLBPointon added the bug Something isn't working label Jun 13, 2023
@DLBPointon
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DLBPointon commented Jun 13, 2023

CDS seems most reliable, however, not in some cases for birds.
CDNA track is just not suitable for use with how the naming comes across. GalGal 7b seems to be bad for this.

@DLBPointon DLBPointon added the Release 2 Issues related to the TreeVal 2.0 label Jul 6, 2023
@muffato muffato added this to the Release 2 milestone Sep 25, 2023
@DLBPointon
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This is linked to #151

As part of the validator, I am adding in some fasta parsing functionality for parsing the geneset data.

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