Good Morning Boris:
If you have the mysql command available on your system, you
can perform the following mysql query to fetch this information:
$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A \
-e "select genoName,genoStart,genoEnd,repName,genoEnd-genoStart,strand
from rmsk limit 4;" hg19
+----------+-----------+---------+-----------+-------------------+--------+
| genoName | genoStart | genoEnd | repName | genoEnd-genoStart | strand |
+----------+-----------+---------+-----------+-------------------+--------+
| chr1 | 10000 | 10468 | (CCCTAA)n | 468 | + |
| chr1 | 10468 | 11447 | TAR1 | 979 | - |
| chr1 | 11503 | 11675 | L1MC | 172 | - |
| chr1 | 11677 | 11780 | MER5B | 103 | - |
+----------+-----------+---------+-----------+-------------------+--------+
Or, using the table browser, select the "output format:" as:
"selected fields from primary and selected tables"
and check the columns as indicated above.
--Hiram
Boris Joffe wrote:
> Dear colleagues,
>
> I would like to collect the information about the distribution of
> repeats over chromosomes.
> That is, in which position of the chromosome a given repeat (hit) starts
> and ends. I do not care about strands, that is, real direction of the
> repeat makes no difference to me. Important for me is that
>
> (1) myStart and myEnd describe the position of a given hit in the
> chromosome and
>
> (2) myEnd - myStart (+/- 1, if necessary)
> gives the length of the hit.
>
> A table showing what I download is attached. I failed to understand
> (even after browsing through help and this list) which fields I should
> use and how.
>
> I would be very grateful for help
>
> Boris Joffe
>
> =============================
> Dr. B.Joffe
> Biozentrum (LMU)
> Grosshaderner Str. 2
> Planegg-Martinsried
> 82152 Germany
>
> [email protected]
> tel. (0)89 2180 74 223
> fax (0)89 2180 74 236
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