Repeat Masker BED file

[Marco Matejcic]

Good morning

 

My name is Marco Matejcic and I’m a postdoc fellow at IARC, in France.

 

I’ve got a question in relation to the Repeat Masker database.

 

When I download RepeatMask as BED file from UCSC website (see screenshot attached), I get a file with only four columns:

 

chr1	16777160	16777470	AluSp	2147	+
chr1	25165800	25166089	AluY	2626	-
chr1	33553606	33554646	L2b	626	+
chr1	50330063	50332153	L1PA10	12545	+
chr1	58720067	58720973	L1PA2	8050	-
chr1	75496180	75498100	L1MB7	10586	+

 

However, when I click on the “Describe table schema” box in the attached screenshot, I can see a more complete description for each line:

 

bin	swScore	milliDiv	milliDel	milliIns	genoName	genoStart	genoEnd	genoLeft	strand	repName	repClass	repFamily	repStart	repEnd	repLeft	id
585	1504	13	4	13	chr1	10000	10468	-249240153	+	(CCCTAA)n	Simple_repeat	Simple_repeat	1	463	0	1
585	3612	114	270	13	chr1	10468	11447	-249239174	-	TAR1	Satellite	telo	-399	1712	483	2
585	437	235	186	35	chr1	11503	11675	-249238946	-	L1MC	LINE	L1	-2236	5646	5449	3
585	239	294	19	10	chr1	11677	11780	-249238841	-	MER5B	DNA	hAT-Charlie	-74	104	1	4

 

How can I download a file including all the columns listed above?

 

Thanks for your help

 

Marco

[Jonathan Casper]

Hello Marco,

Thank you for your question about retrieving the full contents of the RepeatMasker table. In your screenshot, it shows that you have selected the output format "BED - Browser Extensible Data". The BED output for this track from the UCSC Table Browser is a simplified representation of the data, and is not intended to contain all of the information listed by the "describe table schema" button. There are a couple of ways for you to obtain all of the data listed by "describe table schema".

The first method is to use the UCSC Table Browser as in your screenshot, but change the output format to "all fields from selected table". The output of that search will contain all of the fields listed by "describe table schema". It is important to note, though, that it will contain about 450 MB of uncompressed data.

The second option is to download the file http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/rmsk.txt.gz, and the accompanying http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/rmsk.sql. The first file is a compressed version of the data that you would get from the UCSC Table Browser - it is around 137 MB instead of 450 MB. You will need a decompression program to extract the data from this file. The second file (rmsk.sql) contains a short description of the fields that appear in the data, very similar to the description that you see when you click the "describe table schema" button.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

--
Jonathan Casper
UCSC Genome Bioinformatics Group

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