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MD-Anderson-Bioinformatics / SpliceSeq

A tool for investigating alternative mRNA splicing in next generation mRNA sequence data.
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Need protein sequences for TCGA SpliceSeq splice events/Unable to download SpliceSeq #12

Open srcrowl opened 6 months ago

srcrowl commented 6 months ago

I have been using data from TCGA SpliceSeq, and would like to obtain the protein sequences associated with each of the splice events in the database, but this data does not appear downloadable (or I cannot find it). I attempted to download SpliceSeq to dig deeper into the splicegraph that way, but was unable to download (similar issues as other posted issues). Any help or suggestions would be appreciated with how to extract this information from the provided data.

juicenotbad commented 3 weeks ago

hi, how is the problem going? I encountered the same cercumstances.

srcrowl commented 2 weeks ago

Unfortunately, I ultimately did not solve this issue, and moved forward with the information that is currently available

juicenotbad commented 1 week ago

what a pity! thanks for informing, good luck!

ChrisWakefield commented 1 day ago

See new changes to https://bioinformatics.mdanderson.org/public-software/spliceseq/installation/ with functioning links for both SpliceSeq.zip and SpliceGraphDB (which now links to TCGA_SpliceGraph.zip).

Regarding your goal of "the protein sequences associated with each of the splice events", my reading of both the cited article and the Data Loading page state the transcripts were from Ensembl. https://doi.org/10.1093/bioinformatics/bts452 https://bioinformatics.mdanderson.org/public-software/spliceseq/dataloading/

This may be way too late for some, but I hope it helps. Please let me know.