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AlexsLemonade / identifier-refinery

Tools and assets for easy gene identifier conversion
https://github.com/AlexsLemonade/identifier-refinery
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Use transcriptcluster.db instead of probeset.db for ST arrays #7

Closed jaclyn-taroni closed 6 years ago

jaclyn-taroni commented 6 years ago

Closes #5. Turns out that those probe ids are correct/the platform design packages followed the same general format. It was the lack of overlap with the mappings in the probeset.db package that was the issue. I've moved to using the more "gene-centric" transcriptcluster.db packages. Here's what the head of ragene10st.tsv looks like now:

PROBEID ENSEMBL SYMBOL ENTREZID UNIGENE REFSEQ
10918791 ENSRNOG00000005970 Lrrc1 367113 Rn.15622 NM_001014268
10918791 ENSRNOG00000005970 Lrrc1 367113 Rn.15622 NP_001014290
10805165 ENSRNOG00000051965 Smad4 50554 Rn.9774 NM_019275
10805165 ENSRNOG00000051965 Smad4 50554 Rn.9774 NP_062148
10828440 ENSRNOG00000000471 B3galt4 171079 Rn.24575 NM_133553
10828440 ENSRNOG00000000471 B3galt4 171079 Rn.24575 NP_598237
10889331 ENSRNOG00000059402 Itgb1bp1 298914 Rn.29469 NM_001106719
10889331 ENSRNOG00000059402 Itgb1bp1 298914 Rn.29469 NP_001100189
10889331 ENSRNOG00000059402 Itgb1bp1 298914 Rn.29469 XM_006239979
10889331 ENSRNOG00000059402 Itgb1bp1 298914 Rn.29469 XM_006239980
Miserlou commented 6 years ago

Looks great, does this mean we are dropping support for huex10st, moex10st and raex10st?

Also, I assume that after merge, this requires a re-build, re-Zenodo-ing and re-imagebuilding?

jaclyn-taroni commented 6 years ago

does this mean we are dropping support for huex10st, moex10st and raex10st?

These were not in supported platforms, so I figured I would remove them while I was at it.

Also, I assume that after merge, this requires a re-build, re-Zenodo-ing and re-imagebuilding?

Yes, I have the zip file ready to go. You may have to be the one to update Zenodo unless I can figure out a way for you to invite me as a collaborator on the record or something -- have not found a solution yet.