Get list of LINE1 elements as a bed file

Question

[sebastianzeki0]

I would like to get a bed file which describes start and end positions of all LINE1 elements. How can I get this off either RepeatMasker or UCSC browser?

Answer 1

[Pierre Lindenbaum]

$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 -e 'select chrom,chromStart,chromEnd,name from nestedRepeats where repClass="LINE" '
+-------+------------+----------+--------+
| chrom | chromStart | chromEnd | name   |
+-------+------------+----------+--------+
| chr1  |      23803 |    24448 | L2b    |
| chr1  |      26582 |    27137 | L2c    |
| chr1  |      38058 |    40626 | L2a    |
| chr1  |      43242 |    45753 | L1MA8  |
| chr1  |      54464 |    55608 | L2     |
| chr1  |      61695 |    62229 | L1M5   |
| chr1  |      71368 |    78235 | L1MC4a |
| chr1  |      72184 |    72897 | L1PA7  |
| chr1  |      73844 |    76697 | L1PA2  |
| chr1  |      78231 |    78890 | L1M2   |
(...)
+-------+------------+----------+--------+

Answer 2

[Alex Reynolds]

See: https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/mxN2vTRmVks/Ij6lQg_xWEQJ