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# Creating the NuMTs track for hg38 (Done ogress 2014-09-03 Megna Chalamala

cd public_html
mkdir tracks
cd tracks
mkdir hub (renaming to NUMTs soon)
cd hub
wget https://raw.githubusercontent.com/Koumokuyou/NUMTs/main/genomes.txt
wget https://raw.githubusercontent.com/Koumokuyou/NUMTs/main/hub.txt
mkdir hg38
cd hg38
wget https://raw.githubusercontent.com/Koumokuyou/NUMTs/main/hg38/NUmts.html
wget https://raw.githubusercontent.com/Koumokuyou/NUMTs/main/hg38/trackDb.txt
# download NUMTs_hg38.bb into local computer
# open new terminal window
# log in to sftp
put /Users/megnachalamala/NUMTs_hg38.bb /cluster/home/mchalama/public_html/tracks/NUMTs/hg38
# open genome browser
# navigate to custom hub and paste the following URL
https://hgwdev.gi.ucsc.edu/~mchalama/tracks/NUMTs/hub.txt

# Create into a UCSC track from the hub
cd /hive/data/genomes/hg38/bed/
mkdir nuMtSeq
# Grab the bigBed file
wget https://hgwdev.gi.ucsc.edu/~mchalama/tracks/NUMTs/hg38/NUMTs_hg38.bb
mv NUMTs_hg38.bb nuMtSeq/nuMtSeq_hg38.bb
# Place in the proper location
ln -s /hive/data/genomes/hg38/bed/nuMtSeq/nuMtSeq_hg38.bb /gbdb/hg38/bbi/nuMtSeq/nuMtSeq_hg38.bb
