Self Alignments Track Settings
 
Alignments of Other Repeat Browser Consensuses   (All Annotations of Repeat Consensuses tracks)

Display mode:   

Alignment Gap/Insertion Display Options Help on display options
Draw double horizontal lines when both genome and query have an insertion
Draw a vertical purple line for an insertion at the beginning or end of the
query, orange for insertion in the middle of the query
View table schema

Description

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.

Display Conventions and Configuration

The track is stored as a bigPsl. See above for coloring options. Solid bars are region of alignment, breaks are insertions or deletions.

Methods

The collection of consensus sequences was aligned against itself with blat.

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

References

Email: jferna10@ucsc.edu or mhaeussl@ucsc.edu