Remove support for UCSC transcripts

Question

Remove support for UCSC transcripts

holtgrewe opened this issue 4 years ago · 5 comments

Is your feature request related to a problem? Please describe.
I think the create more problems than they solve as they provide a third alignment of transcripts to the reference. RefSeq and ENSEMBL are enough.

Describe the solution you'd like
Remove support for them in code and documentation.

Describe alternatives you've considered
N/A

Additional context
N/A

Answer 1 · 2021-06-09T08:25:32.000Z

@pnrobinson what do you think?

Answer 2 · 2021-06-09T13:12:19.000Z

Why don't we fix the current bug with building the ser files, leave out UCSC, and if it turns out people really want to have it we can add back support later on?

Answer 3 · 2021-06-09T20:48:40.000Z

Sounds good to me.

Answer 4 · 2021-06-09T20:49:15.000Z

Actually, there is no bug in building the .ser files but a bug in the alignment projection... It turns out you should look at the number of bases in the transcript rather than in the reference when checking your alignments.

Answer 5 · 2021-06-18T16:27:03.000Z

Can we keep UCSC support? The UCSC data is stable (to my knowledge) so shouldn't cause a maintenance burden. I thought the projection bug was for RefSeq data as this is the one which required the alignment objects?

I'm obviously motivated by Exomiser maintenance and UCSC is provided as an option for people to use. I don't know how many people use this option, however.