mysql command to download mm9 Mappability tables from Mapping and Sequencing

Question

[Shicheng Guo]

Hi All,

Anyone can share the mysql command to download 'Mappability' tables from 'Mapping and Sequencing' group?

check the link of 'Mappability'

Sincerely,

Answer 1

[Pierre Lindenbaum]

$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 -e 'show tables like "%ability%"'
+------------------------------------------+
| Tables_in_hg19 (%ability%)               |
+------------------------------------------+
| wgEncodeCrgMapabilityAlign100mer         |
| wgEncodeCrgMapabilityAlign24mer          |
| wgEncodeCrgMapabilityAlign36mer          |
| wgEncodeCrgMapabilityAlign40mer          |
| wgEncodeCrgMapabilityAlign50mer          |
| wgEncodeCrgMapabilityAlign75mer          |
| wgEncodeDacMapabilityConsensusExcludable |
| wgEncodeDukeMapabilityRegionsExcludable  |
| wgEncodeDukeMapabilityUniqueness20bp     |
| wgEncodeDukeMapabilityUniqueness35bp     |
+------------------------------------------+

.

$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 -e 'desc wgEncodeDukeMapabilityUniqueness35bp'
+----------+--------------+------+-----+---------+-------+
| Field    | Type         | Null | Key | Default | Extra |
+----------+--------------+------+-----+---------+-------+
| fileName | varchar(255) | NO   |     | NULL    |       |
+----------+--------------+------+-----+---------+-------+

it's just a path to a bigwig file in the UCSC server

$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 -e 'select * from wgEncodeDukeMapabilityUniqueness35bp'
+------------------------------------------------------------+
| fileName                                                   |
+------------------------------------------------------------+
| /gbdb/hg19/bbi/wgEncodeDukeMapabilityUniqueness35bp.bigWig |
+---------

---------------------------------------------------+

the public file that is available here:

http://hgdownload.soe.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/wgEncodeDukeMapabilityUniqueness35bp.bigWig

and you can use the UCSC executables to handle/quert this file.