This track shows alignments between consensus sequences from the Repeat Browser. This allows one to see how sequences are related to one another and identify deletions or insertions between classes of elements.
The track is stored as a bigPsl. See above for coloring options. Solid bars are region of alignment, breaks are insertions or deletions.
blat ../hg38reps/hg38reps.fa ../hg38reps/hg38reps.fa other_cons_aln.psl
pslToBigPsl other_cons_aln.psl stdout | sort -k1,1 -k2,2n > other_cons_aln.txt
wget https://genome.ucsc.edu/goldenPath/help/examples/bigPsl.as
bedSort other_cons_aln.txt other_cons_aln.txt
bedToBigBed as=bigPsl.as -type=bed12+13 -tab other_cons_aln.txt ../hg38reps/hg38reps.sizes other_cons_aln.bb
Email: jferna10@ucsc.edu or mhaeussl@ucsc.edu