column's meaning of Alu element bed file

[Wenbin Guo]

Dear UCSC staff,

Thank you for your service. I tried to extract the Alu elements' coordinates from the genome browser. Therefore I selected the following options in the Table Browser.

clade: mammal, genome: human, assembly: hg38

group: repeats, track: RepeatMasker

table: rmsk

region: genome

filter: repFamily does match "Alu" (without the quotes)

Output format: BED; plain text

get BED

It returns a tab-separated table like this:

chr1	8388315	8388618	AluY	2582	-

The columns represent chromosome, start, end, name etc. I am a little confused about the meaning of the 5th column, 2582,  may I ask what does it mean?

Thanks,
Wenbin

[Gerardo Perez]

Hello, Wenbin.

Thank you for your interest in the Genome Browser and for your question about the 5th column in the BED output format.

The 5th column in a BED format is the score field. For more information on BED fields, see the following help page: https://genome.ucsc.edu/FAQ/FAQformat.html#format1.

In the case of the RepeatMasker table, swScores are put into the 5th column. The swScore is the Smith-Waterman alignment score between the repeat element template sequence, from the RepBase library, and the genomic sequence. For more information on RepeatMasker and its output, see the following help page: http://www.repeatmasker.org/webrepeatmaskerhelp.html#reading. For more information on the RepBase Library, see the following page: http://www.girinst.org/repbase/update/index.html.

You can also change the output format to "all fields from selected table". The output of that search will contain all of the fields of the table and the corresponding column name.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute

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[Wenbin Guo]

Thank you very much! It's very useful!

Best,

Wenbin