# Mouse Development Timecourse bulk RNA-seq (2026-04-10 Gerardo)
# Converting track hub from Wold Lab (Caltech) into native tracks.
# Hub URL: http://woldlab.caltech.edu/~diane/mouse_development_bulk/mouse_development.hub.txt
# Publication: https://www.encodeproject.org/publications/e0d01543-9965-4edb-933c-778a40575cd9/
# mm39 data are liftOver'd from mm10 GENCODE M21 alignments.
# 17 tissues, up to 8 timepoints (e10.5-e16.5, P0), two replicates per condition.
# bigBarChart tracks with FPKM and TPM from RSEM.

# Download data files from hub to /hive/data/outside/
mkdir -p /hive/data/outside/woldlab/mouseDevTimecourse/mm39
cd /hive/data/outside/woldlab/mouseDevTimecourse/mm39

for f in mouse_development_TPM_M21_mm39.bb mouse_development_FPKM_M21_mm39.bb \
    mouse_development_M21.categories mouse_development_M21.facets; do
    curl -o "$f" "http://woldlab.caltech.edu/~diane/mouse_development_bulk/$f"
done

# Create symlinks in /gbdb/mm39/
mkdir -p /gbdb/mm39/mouseDevTimecourse
cd /gbdb/mm39/mouseDevTimecourse
for f in /hive/data/outside/woldlab/mouseDevTimecourse/mm39/*; do
    ln -s "$f" .
done

# Add trackDb entry
cd ~/kent/src/hg/makeDb/trackDb/mouse/mm39
# Created mouseDevTimecourse.ra (superTrack with 2 bigBarChart subtracks)
# Created HTML description files:
#   mouseDevTimecourse.html (supertrack)
#   developmentTimecourseM21mm39TPM.html
#   developmentTimecourseM21mm39FPKM.html
# Added "include mouseDevTimecourse.ra" to trackDb.ra

# Load trackDb
cd ~/kent/src/hg/makeDb/trackDb
make DBS=mm39
##############################################################################
