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legumeinfo / datastore-issues

mostly for issues pertaining to the content of the legumeinfo datastore; may also relate to characteristics of its user interface or managing the mirroring process to the legfed instance
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expression data for cowpea pangenome #127

Closed adf-ncgr closed 1 year ago

adf-ncgr commented 2 years ago

per discussion, we have TPM data for both the set of samples from a given cultivar mapped back to its own genome as well as all mapped to the main reference genome. You'll find the latter under: /erdos/adf/nf-core/rnaseq/cowpea_pangenome_rnaseq.all_together_markdups/star_salmon and the former under folders in the same location (one for each of the non-reference cultivars): cowpea_pangenome_rnaseq.CB5-2 cowpea_pangenome_rnaseq.Sanzi cowpea_pangenome_rnaseq.Suvita2 cowpea_pangenome_rnaseq.TZ30 cowpea_pangenome_rnaseq.UCR779 cowpea_pangenome_rnaseq.ZN016

since you volunteered to datastorify these, I happily pass the buck to you @sammyjava ! Just let me know if you have any questions...

adf-ncgr commented 2 years ago

need to check whether I updated metadata, there was an issue with a couple of labels having been swapped in the SRA submission that Tim helped resolve, I think I applied it locally as well but will verify

adf-ncgr commented 2 years ago

OK, I just figured out what was confusing me about this and the correction made by Tim at NCBI. The way that they submitted the data all of the experiments for a given lines link to the same sample accession, while the experiment descriptors give the correct information about tissue and treatment. So please do use the metadata that has been corrected locally in any of the files under /erdos/adf/nf-core/rnaseq/cowpea_pangenome_rnaseq.CB5-2/samplesheet (and similarly for the other accessions which didn't require any corrections, although they all have a similar issue in that the same sample accession is used for all the different experiments, so it is the experiment descriptor that has the appropriate metadata).

sammyjava commented 1 year ago

These expression studies are all in CicerMine.