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wenjie1991 / TSVdb

TCGA Splicing Variation Database Cancer Splicing Variant Database Cancer alternative splicing database
http://www.tsvdb.com
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Does not work transcript picture for some genes #29

Closed andreyurch closed 2 years ago

andreyurch commented 4 years ago

I tried 3 different browsers. Cutaneous melanoma, STK19

Screenshot 2020-05-06 at 16 15 39
wenjie1991 commented 4 years ago

Hi @andreyurch, Thanks for reporting this bug!

The gene STK19 has two chromosome location: chr6 and chr6_dbb_hap3. The TSVdb could not deal with those two loations of STK19, thus the bug apeared.

And as the TCGA data only cover the chr6. Therefore, we only include the primary reference chr6 to avoid this error. https://github.com/wenjie1991/TSVdb/commit/4acd2aa0ddb374c709b83e493cb7e7a871dabce6

andreyurch commented 4 years ago

A gene can not be located in two different locations. Yes, there are different annotations, but you can choose a single, the canonical one and visualize it. Why no to correctly visualize transcripts on the chr6?

wenjie1991 commented 4 years ago

Why no to correctly visualize transcripts on the chr6?

Hi @andreyurch. That's what we have done. Maybe I did not make it clear in my last comment. We have updated the code, see commit https://github.com/wenjie1991/TSVdb/commit/4acd2aa0ddb374c709b83e493cb7e7a871dabce6. Now only the canonical chromosomes are used. The case you described has been solved.

andreyurch commented 4 years ago

I apologize for the misunderstanding. Thank you very much!

wenjie1991 commented 4 years ago

You are welcome! Again, thank you for letting us know the bug!