Transcripts of pseudogenes should NOT have the word 'transcript' in name.

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Transcripts of pseudogenes should NOT have the word 'transcript' in name. #1451

Closed monicacecilia closed 7 years ago

monicacecilia commented 7 years ago

Why is the word 'transcript' appearing automatically as part of the name for the transcript of a pseudogene? (see figure below). This should not be the case. Numbering / IDs should be generated in the same way IDs are generated for transcripts of coding-genes.

screen shot 2017-01-24 at 3 33 04 pm

monicacecilia commented 7 years ago

Actually, the same seems is true for all other annotated genomic elements. I don't recall when this change was introduced. Refreshers? Why? It should not be the case.

nathandunn commented 7 years ago

@monicacecilia To clarify:

gene and mRNA naming is correct
[x] all non-coding transcripts should be named as mRNA's with their corresponding pseudogenes being names similar to a regular gene
transposable_elements and repeat_region should continue to be named as they are currently (basically just getting a hash)

Not sure that any of this is new, but I agree that the "transcript" suffix is weird and should be fixed.

deepakunni3 commented 7 years ago

@nathandunn I agree. I can work on this and probably add some tests as well to make sure our naming service generates the proper name formats.

nathandunn commented 7 years ago

Awesome thanks @deepakunni3