Details
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Type:
Improvement
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Status: To-Do (View Workflow)
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Priority:
Major
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Resolution: Unresolved
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:2
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Epic Link:
Description
Situation: The GenArk Genomes IGB App adds thousands of genome assemblies from UCSC GenArk. Many of these assemblies use technical chromosome names that are not always human readable friendly. In the GenArk paper they state:
GenArk provides a new sequence name translation system that allows using either NCBI GenBank accessions, NCBI RefSeq accession, or the more familiar sequence names in their UCSC or Ensembl format (chrM=MT, chr1=1, chrY=Y, respectively) for position searches, custom tracks, and track hubs. This means that rewriting of the “sequence name” field of all annotation files is no longer necessary.
IGB similarly has a way to add personal synonyms such as a chromosome.txt that allows IGB to relate different names for chromosomes, such as Chr1 = chr1 = 1.
Task: Investigate how IGB could utilize the chromAlias.txt file provided as part of the GenArk hub to add chromosome aliases.
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-4086 [ 23382 ] |