Planned Release: V18

[jharenza]

What data file(s) does this issue pertain to?

pbta-histologies.tsv
all RNA-Seq files

What release are you using?

V17

Put a link to the relevant section of the OpenPBTA-manuscript here.

NA

Put your question or report your issue here.

Some future updates to include:
Add 8 RNA-Seq samples #749:

• pbta-star-log-final.tar.gz

• pbta-star-log-manifest.tsv

• pbta-mend-qc-manifest.tsv

• pbta-mend-qc-results.tar.gz

• pbta-isoform-counts-rsem-expected_count.stranded.rds

• pbta-isoform-expression-rsem-tpm.stranded.rds

• pbta-fusion-arriba.tsv.gz

• pbta-fusion-putative-oncogenic.tsv

• pbta-fusion-recurrently-fused-genes-byhistology.tsv

• pbta-fusion-recurrently-fused-genes-bysample.tsv

• pbta-fusion-starfusion.tsv.gz

• pbta-gene-counts-rsem-expected_count.stranded.rds

• pbta-gene-expression-kallisto.stranded.rds

• pbta-gene-expression-rsem-fpkm-collapsed.stranded.rds

• pbta-gene-expression-rsem-fpkm.stranded.rds

• pbta-gene-expression-rsem-tpm.stranded.rds

• independent-specimens.rnaseq.primary-plus-stranded.tsv

• fusion_summary_lgat_foi.tsv

• md5sum.txt

• Add new medulloblastoma subtype pathology results file Medulloblastoma pathology subtypes: file for data release #746

• pbta-histologies.tsv refresh (V18 or maybe V19, post rework of subtyping modules post Planned Data Release: V17 #732 to use pathology_diagnosis and free_text_dx due to being stuck in a loop for Update/Create SQL rules for integrated diagnosis, broad, and short histologies #748)

• Add Extent of Tumor Resection to pbta-histologies.tsv cc @adamcresnick and @baileyckelly

[jaclyn-taroni]

We're going to need to update the following files, because the tumor_descriptor field is changing in v17:

independent-specimens.wgs.primary-plus.tsv
independent-specimens.wgs.primary.tsv
independent-specimens.wgswxs.primary-plus.tsv
independent-specimens.wgswxs.primary.tsv

Regenerating those files is tracked in #767.

Edit: Now that #781 has been merged, the files listed above should be updated in v18 using the files that are in the master branch here: https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/independent-samples/results

[jaclyn-taroni]

pbta-fusion-recurrent-fusion-byhistology.tsv will also need to be updated because of the tumor_descriptor change - tracked in #769.

Edit: Now that #744 has gone in, the analysis fusion files included in the data release should be updated to use what is in the master branch here: https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/fusion_filtering/results

Those files are:

pbta-fusion-putative-oncogenic.tsv
pbta-fusion-recurrently-fused-genes-byhistology.tsv
pbta-fusion-recurrently-fused-genes-bysample.tsv

[jharenza]

@jaclyn-taroni we are going to aim to release all RNA files listed here, plus fusion_summary_lgat_foi.tsv, and the independent specimens files Monday 11/23/20

For pbta-histologies.tsv, we will not have the new rules for broad/short histology/integrated dx because several subtyping modules are ongoing. We will add subtypes based on whatever subtyping modules have been merged by Friday/Monday.

cc @kgaonkar6