56c1481dcd7988e497207c1a69bda2da42e986d0 max Tue Mar 10 04:03:37 2026 -0700 docs change after claude diff --git src/hg/makeDb/doc/hg38/mpravardb.txt src/hg/makeDb/doc/hg38/mpravardb.txt index f3305f0414b..f121a767414 100644 --- src/hg/makeDb/doc/hg38/mpravardb.txt +++ src/hg/makeDb/doc/hg38/mpravardb.txt @@ -1,22 +1,22 @@ # MPRAVarDB track -# Mon Mar 10 2026 (max) +# Mon Mar 10 2026 (claude/max) # Download data from https://mpravardb.rc.ufl.edu/ mkdir -p /hive/data/genomes/hg38/bed/mpra/mpravardb cd /hive/data/genomes/hg38/bed/mpra/mpravardb +wget 'https://mpravardb.rc.ufl.edu/session/27d7af46df917aed91f4cca7bee378a2/download/download_all?w=' -O mpravardb.csv -# The file mpravardb.csv was downloaded from the MPRAVarDB website. # 242,818 variants from 18 MPRA studies, with both hg19 and hg38 coordinates. # 213,689 are hg19, 29,129 are hg38, 3,676 have no coordinates (NA). # Convert to BED, liftOver hg19->hg38, merge, and create bigBed: python3 ~/kent/src/hg/makeDb/scripts/mpravardb/mpravardbToBed.py # Output: mpravardb.bb (239,028 variants after liftOver, 114 unmapped) # Create gbdb symlink mkdir -p /gbdb/hg38/mpra ln -sf /hive/data/genomes/hg38/bed/mpra/mpravardb/mpravardb.bb /gbdb/hg38/mpra/mpravardb.bb # Rebuild trackDb cd ~/kent/src/hg/makeDb/trackDb make DBS=hg38