Data release/add v5 release

[yuankunzhu]

Purpose/implementation

data release updates for v5

• changes:
  • Separated RNA-Seq files:
    • Created separate RDS files for stranded and polyA RNA-Seq samples
  • new RNA-Seq counts files:
    • Added RSEM count matrices for genes and transcripts
  • new ARRIBA file:
    • Add annots column header which was removed during FusionAnnotator run
  • new SNV files:
    • Add Lancet VEP-annotated MAF
    • Add VarDict VEP-annotated MAF
  • new BED interval files:
    • Add WXS BED (same file used for each variant caller)
    • Add WGS BED files for each variant caller
    • Methods described here.

Issue/Caveats

• Expression filename has been changed, some R/Rmd script might be failed like:

  • OpenPBTA-analysis/analyses/transcriptomic-dimension-reduction/02-dimension-reduction.sh

    Line 24 in e5a8700

    --expression ../../data/pbta-gene-expression-rsem.fpkm.rds \

  • OpenPBTA-analysis/analyses/transcriptomic-dimension-reduction/01-subset-expression-by-strategy.R

    Line 36 in e5a8700

    "pbta-gene-expression-rsem.fpkm.rds")

  • OpenPBTA-analysis/analyses/create-subset-files/01-create_subset_files.Rmd

    Line 124 in 6e3405e

    rsem_file <- "pbta-gene-expression-rsem.fpkm.rds"

• still missing/working on transcripts count, @jharenza suggested we do the PR for now, and add that once it's ready and update checksum then.

Directions for reviewers

changed on release notes and download script.

• file content updated for pbta-fusion-arriba.tsv.gz and md5sum.txt.
• add file *.polya.rds, *.stranded.rds, *.bed pbta-snv-lancet.vep.maf.gz and pbta-snv-vardict.vep.maf.gz
• remove file pbta-gene-expression-kallisto.rds and pbta-gene-expression-rsem-fpkm.rds

Results

Docker and continuous integration

[jaclyn-taroni]

I can confirm that I can successfully run bash download-data.sh with this branch checked out.

[jaclyn-taroni]

Thanks for noting the breaking changes @yuankunzhu. We will not have issues with the tests breaking at the moment because until I tackle #124 (hopefully today or tomorrow) the files specifically for testing will be tied to the v4 release.

[jaclyn-taroni]

@yuankunzhu this essentially reverts a change introduced in #107. Can you remove this reference to a README please? I would fix myself and merge but I can't push to this branch.

[jaclyn-taroni]

I will make this small change #127 (comment) when I address #124. Merging so folks can get started on their updates.