cd059caf16656b4fba59a5c9b841978293582dab dschmelt Wed Sep 7 13:51:38 2022 -0700 Minor edits to page, refs #29356 diff --git src/hg/htdocs/goldenPath/help/bigRmsk.html src/hg/htdocs/goldenPath/help/bigRmsk.html index ffe9ef3..ab2bf64 100755 --- src/hg/htdocs/goldenPath/help/bigRmsk.html +++ src/hg/htdocs/goldenPath/help/bigRmsk.html @@ -1,70 +1,71 @@

bigRmsk Track Format

The bigRmsk format allows for the display of annotations of a genome generated by the RepeatMasker program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. -

The bigRmsk format enables taking the annotation output of RepeatMasker and converting it into a compressed and indexed bigBed file. Please see this page for a details of the bigBed format, its use, and associated tools.

bigRmsk track definitions

The bigRmsk tracks consist of two bigBed files define by autoSql schema:

The primary bigRmsk file, define by bigRmskBed.as, +
The primary bigRmsk file, define by + bigRmskBed.as, which has the annotations of repeats. -
The secondary bigRmskAlign file, define by bigRmskAlignBed.as, - which contains the alignments of the consensus repeats to the genome. This file is optional, if omitted, - the bigRmsk track will function, without the ability to view the alignments. +
The secondary bigRmskAlign file, define by + bigRmskAlignBed.as, + which contains the alignments of the consensus repeats to the genome. This file is optional, + if omitted, the bigRmsk track will function, without the ability to view the alignments.

- The input files for the bigRmsk files are create from the RepeatMasker *.out and *.align files - using the rmToTrackHub.pl program that is include with RepeatMasker. The bigRmsk + The input files for the bigRmsk files are created from the RepeatMasker *.out and + *.align files + using the rmToTrackHub.pl program that is included with RepeatMasker. The bigRmsk format is not designed to work with any other type of data.

Creating a bigRmsk track

- To create a bigRmsk track, and its supporting files, follow the below steps. + To create a bigRmsk track and its supporting files, follow the below steps. This assumes that you have already run RepeatMasker and have a *.out, and optionally *.align file.

- RepeatMasker output files are convert to the bigRmsk textual form using the + RepeatMasker output files are converted to the bigRmsk textual form using the RepeatMasker/util/rmToTrackHub.pl program that is part of the RepeatMasker distribution.

- NOTE: The current version of RepeatMasker (4.1.2-p1) does not contain the - rmToTrackHub.pl program. Until it is available in, obtain a copy + NOTE: The April 2021 version of RepeatMasker (4.1.2-p1) does not contain the + rmToTrackHub.pl program. Until it is included, obtain a copy from the RepeatMasker GitHub development branch:

       
       git clone -b development git@github.com:rmhubley/RepeatMasker.git

Step 1. If you wish to experiment with quickly building an example track, download the example RepeatMasker output files for the human GRCh38 (hg38) assembly bigRmskExample.out and bigRmskExample.align used in this tutorial: