repeatMasker

[Yuan Jian]

Hello,

I have downloaded hg38 repeatMasker. I can understand the categories: LINE, LTR SINE etc.

could you please tell me what the meaning of the categories: scRNA, srpRNA, snRNA, RC, DNA and RNA?

thanks

Yuan Yu

[Matthew Speir]

Hi Yuan,

Thank you for your question about the RepeatMasker track for hg38. These different names represent different classes and families of repeats identified by the RepeatMasker program using the RepeatMasker version of the Repbase Update database.

You can find more information about the RepeatMasker track on the description page, http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=rmsk, and you can information on the structure of the "rmsk" (RepeatMasker) table and what its different columns represent here: http://genome.ucsc.edu/cgi-bin/hgTables?db=hg38&hgta_group=rep&hgta_track=rmsk&hgta_table=rmsk&hgta_doSchema=describe+table+schema, or by clicking the "View table schema" link on the description page linked previously.

You can find more information about Repbase Update here: http://www.girinst.org/repbase/, and you can search their database here: http://www.girinst.org/repbase/update/search.php. Note that RepeatMasker uses a special version of the Repbase Update database, so you may want to use the "Search for Repeat Masker edition sequence" search box.

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.

Matthew Speir
UCSC Genome Bioinformatics Group

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