cognoma / cancer-data

TCGA data acquisition and processing for Project Cognoma
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Invalid gene in mutation-matrix.tsv.bz2 on figshare v5 #36

Closed dhimmel closed 7 years ago

dhimmel commented 7 years ago

See https://github.com/cognoma/core-service/pull/42#discussion_r91731695, where @stephenshank has discovered a gene with an invalid entrez_gene_id in mutation-matrix.tsv.bz2 from https://doi.org/10.6084/m9.figshare.3487685.v5.

The gene is 117153, which is not included in genes.tsv.

dhimmel commented 7 years ago

@stephenshank I figured out the issue :crossed_fingers::

So hopefully if you update to version 6 the issues will be fixed. Sorry about that -- my bad with not updating the figshare.

@vasudevanv, this is the sort of mistake that continuous deposition would solve -- basically any time the cancer-data code is updated the datasets are regenerated and uploaded to figshare. Not that this is worth the time to implement, but it's the way of the future.