Thursday, October 31, 2013

v26 (2 of 3): RepeatMasker tracks

A minor update to RepeatMasker tracks has been made, which is the ability to grade repetitive elements by their Smith-Waterman alignment scores.

The updated RepeatMasker tracks are available for following genomes: hg18, hg19, mm9, mm10, rn4, danRer7, dm3. All the RepeatMasker track data were downloaded from UCSC Genome Browser.

Go to browser and show human hg19 genome. At Tracks > Genomic annotation tracks > RepeatMasker, you can see a long list of tracks. Each track is one "class" of repeats, click the arrow following the track to see tracks of families from this class:


Click track L1 (LINE) to display it, which is the "L1" family from "LINE" class:



The L1 elements in above screenshot show various shades of color, which are determined by the greatest SW score of all L1 elements in the view range. Click on an element to see details:


Right click on the L1 track and choose "Configure". You can find options about what kind of scores can be used to grade the elements, or you can choose to disable the score and all items will become fully visible: