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mysql command to download mm9 Mappability tables from Mapping and Sequencing

Hi All,

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

check the link of 'Mappability'

Sincerely,

mapping and sequencing mappability

1 answer

$ 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.

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