8c520f540bf2410ce30bbf71f16f292b90144a5a Merge parents cd059ca 11bfdf3 dschmelt Wed Sep 7 14:06:50 2022 -0700 Fixing merge, going with markD's changes refs #29356 diff --cc src/hg/htdocs/goldenPath/help/bigRmsk.html index ab2bf64,72eac77..839b9ea --- src/hg/htdocs/goldenPath/help/bigRmsk.html +++ src/hg/htdocs/goldenPath/help/bigRmsk.html @@@ -1,79 -1,70 +1,73 @@@

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. + It is the recommend method of adding RepeatMaster tracks to assembly hubs. + For a descriptions of this features of this track type, with examples, see + standard bigRmsk track description. +

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

- 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: + RepeatMasker output files are convert to the bigRmsk textual form using the + RepeatMasker/util/rmToTrackHub.pl program that is part of the + RepeatMasker 4.1.3 or newer distribution.

-       
-       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:

      
        wget https://genome.ucsc.edu/goldenPath/help/examples/bigRmskExample.out
        wget https://genome.ucsc.edu/goldenPath/help/examples/bigRmskExample.align

Otherwise, substitute your *.out and *.align in theses instructions.