Create v13 RNA-Seq merged matrices

[jharenza]

All RNA-Seq processing is now complete. Please create v13 merged matrices for the below items and deposit into s3://d3b-openaccess-us-east-1-prd-pbta/open-targets/v13/ with an md5sum.txt file.

• [ ] gene-expression-rsem-tpm-collapsed.rds ** highest priority
• [ ] rna-isoform-expression-rsem-tpm.rds
• [ ] gene-counts-rsem-expected_count-collapsed.rds
• [ ] fusion-starfusion.tsv.gz
• [ ] fusion-annoFuse.tsv.gz
• [ ] fusion-arriba.tsv.gz
• [ ] splice-events-rmats.tsv.gz

The NBL/PPTC samples are all now included in the histologies base file here: https://github.com/d3b-center/histologies-qc/blob/c169498c3d32f4a58d5d15c996aa94515de4fc1c/output/2023-05-21_histologies-base.tsv

Note: I put all of the RNA-Seq samples from the NBL/PPTC harmonization in the file, but had to create unique BS_ids for these. I could not use only the model (sample) name since we need a unique bs_id per experimental strategy. In addition, due to all of the clinical data files I was using to compile, I had to update the sample ids slightly. If you can export a manifest from the project (I seem to not be able to do this via GUI easily), I can update the sample ids, and then you can use the histologies file to gather a bs_id per sample_id + experimental strategy to patch metadata and merge.

[jharenza]

I am going to close this in favor of an official release ticket