• Hallmark pathway analysis

Hallmark is curated well (MSigDB) Check for immune library

rGREAT has fixes

• Andrew

• GSCA is bad for ChIP-seq peaks
• TOP-gene, GREAT (MSigDB), rGREAT
• Subsample samples with too many peaks for GREAT

Lee

• List of files for EBV paper to upload to GEO
• pipeline for ChIP-seq data
• In town next week

Philip

• Whole Genome sequencing on Jurkat (sarek pipeline)
• Jurkat cells are mostly European, but cells have too many SNPs (could be cancer)
• TSTV should be around 2

Sift and Polyphen are garbage, I don't care what they say.

• Philip

Diego's suggestion

• Cell line sequencing could be followed by human cell sequencing

Mike Lape

• Nextflow PGSC pipeline is throwing error despite a custom config

Xioting

ChIP-seq QC benchmarks are too subjective? Want to filter public data (can't manually curate).

• #IDR peaks > 500
• Raw peak FRiP of 1% (ENCODE uses this for their method)
• Establish a hard rank cutoff flag