Create a list of seen Ds as part of the normal pipeline

NBISweden / IgDiscover-legacy

Analyze antibody repertoires and discover new V genes from high-throughput sequencing reads

https://www.igdiscover.se

MIT License

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Create a list of seen Ds as part of the normal pipeline #65

Closed marcelm closed 7 years ago

marcelm commented 7 years ago

The discoverj script is unsuitable for that - the results of the plotalleles script are fine (plus an allele ratio filter). Possibly add a discoverd script. It will not really discover anything, only list the used Ds.

marcelm commented 7 years ago

Use Martin’s script (top 500 D cores vs cd-hit)

marcelm commented 7 years ago

This is actually two different tasks:

Determining which known D genes are expressed in the dataset
Discovering novel D genes

The first task has been solved by updating the count subcommand.

The second task has now also been solved by updating the discoverj script to also work for D discovery (it also needs to be renamed).