What is this annotation file format?

Hello, ALL!

I got the following annotation file from UCSC website.

(rmsk.txt in http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/)

However I don't classify this file format. I usually use gtf files as annotation files.

607     12955   105     9       10      chr1    3000000 3002128 -192469843     -       L1_Mus3 LINE    L1      -3055   3592    1466    1
607     1216    268     31      105     chr1    3003152 3003994 -192467977     -       L1Md_F  LINE    L1      -5902   617     1       2

If you know about this file format and how to convert this file to gtf format, please tell me!!

Thank you ALL!

rna-seq

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updated 3.8 years ago by Ram 4.5K • | written 11.3 years ago by cfarmeri 21

Did you read the README?

To see descriptions of the tables underlying Genome Browser annotation
tracks, select the table in the Table Browser:
  http://genome.ucsc.edu/cgi-bin/hgTables?db=mm10
and click the "describe table schema" button.  There is also a "view
table schema" link on the configuration page for each track.

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updated 3.8 years ago by Ram 4.5K • | written 11.3 years ago by Alex Reynolds 3.6K

FYI, according to the README,

Files included in this directory (updated nightly):
  - *.sql files:  the MySQL commands used to create the tables
  - *.txt.gz files: the database tables in a tab-delimited format
    compressed with gzip.

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updated 3.8 years ago by Ram 4.5K • | written 11.3 years ago by Sam 484

1 answer

That's the format produced by repeatMasker. If you want a more useful format, then use the table browser to get a BED or GTF file (though note that both of these incur some information loss, since the table browser doesn't end up including everything).

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updated 3.8 years ago by Ram 4.5K • | written 11.3 years ago by Devon Ryan 10K