# Build trackHub tsv files from the combo* files:
/home/rhubley/projects/RepeatMasker/util/rmToTrackHub2.pl \
  -out combo.out \
  -align combo.align

# Sort tsv files
sort -k1,1 -k2,2n  combo.join.tsv >  combo.join.tsv.sorted
sort -k1,1 -k2,2n  combo.align.tsv >  combo.align.tsv.sorted

# Create chrom.sizes file for assembly
/usr/local/ucscTools/faCount /home/jstorer/T2T_data/genome_assemblies/chm13v2.0.fasta | perl -ne '{ next if ( /
^#|^total/ ); if ( /^(\S+)\s+(\d+)/ ) { print "$1\t$2\n"; } }' > chrom.sizes

# Convert to bigRmskBed and bigRmskAlignBed files
/usr/local/ucscTools/bedToBigBed -tab -as=bigRmskAlignBed.as -type=bed3+14  combo.align.tsv.sorted chrom.sizes 
chm13v2.0_RMSK_ALIGN.bb
/usr/local/ucscTools/bedToBigBed -tab -as=bigRmskBed.as -type=bed9+5 combo.join.tsv.sorted chrom.sizes chm13v2.
0_RMSK.bb