Getting A List Of Satellite Repeats As Bed File From Ucsc [Repeatmasker]

Question: Getting A List Of Satellite Repeats As Bed File From Ucsc [Repeatmasker]

6.2 years ago by

Netherlands

Sukhdeep Singh ♦ 9.5k wrote:

Hi,

I know how to get this list from UCSC, but the problem is the after clicking the "get output", the list to big to be copied. What could be the mysql query for it.

I tried mysql -h genome-mysql.cse.ucsc.edu -A -u genome -D mm9 -e 'select * from rmsk' but got the error

ERROR 1146 (42S02) at line 1: Table 'mm9.rmsk' doesn't exist

Also, in the ucsc downloads page, I am unable to find the rmsk table as a whole genome file (per chromosome exists).

Thanks

repeats mysql repeatmasker • 2.8k views

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modified 4.3 years ago by Biostar ♦♦ 20 • written 6.2 years ago by Sukhdeep Singh ♦ 9.5k

6.2 years ago by

Pierre Lindenbaum ♦ 113k

France/Nantes/Institut du Thorax - INSERM UMR1087

Pierre Lindenbaum ♦ 113k wrote:

the table was split for each chromosome:

   $  mysql -h genome-mysql.cse.ucsc.edu -A -u genome -D mm9 -e 'show tables like "%rmsk"'
    +-----------------------+
    | Tables_in_mm9 (%rmsk) |
    +-----------------------+
    | chr10_rmsk            |
    | chr11_rmsk            |
    | chr12_rmsk            |
    | chr13_random_rmsk     |
    | chr13_rmsk            |
    | chr14_rmsk            |
    | chr15_rmsk            |
    | chr16_random_rmsk     |
    | chr16_rmsk            |
    | chr17_random_rmsk     |
    | chr17_rmsk            |
    | chr18_rmsk            |
    | chr19_rmsk            |
    | chr1_random_rmsk      |
    | chr1_rmsk             |
    | chr2_rmsk             |
    | chr3_random_rmsk      |
    | chr3_rmsk             |
    | chr4_random_rmsk      |
    | chr4_rmsk             |
    | chr5_random_rmsk      |
    | chr5_rmsk             |
    | chr6_rmsk             |
    | chr7_random_rmsk      |
    | chr7_rmsk             |
    | chr8_random_rmsk      |
    | chr8_rmsk             |
    | chr9_random_rmsk      |
    | chr9_rmsk             |
    | chrM_rmsk             |
    | chrUn_random_rmsk     |
    | chrX_random_rmsk      |
    | chrX_rmsk             |
    | chrY_random_rmsk      |
    | chrY_rmsk             |
    +-----------------------+



$ mysql -h genome-mysql.cse.ucsc.edu -A -u genome -D mm9 -e 'select * from chrY_rmsk limit 2\G'
*************************** 1. row ***************************
      bin: 585
  swScore: 477
 milliDiv: 0
 milliDel: 0
 milliIns: 0
 genoName: chrY
genoStart: 95
  genoEnd: 148
 genoLeft: -15902407
   strand: +
  repName: (TC)n
 repClass: Simple_repeat
repFamily: Simple_repeat
 repStart: 1
   repEnd: 53
  repLeft: 0
       id: 1
*************************** 2. row ***************************
      bin: 585
  swScore: 3001
 milliDiv: 210
 milliDel: 22
 milliIns: 28
 genoName: chrY
genoStart: 283
  genoEnd: 1198
 genoLeft: -15901357
   strand: +
  repName: L1_Mur3
 repClass: LINE
repFamily: L1
 repStart: 1060
   repEnd: 1980
  repLeft: -3900
       id: 2

ADD COMMENT • link written 6.2 years ago by Pierre Lindenbaum ♦ 113k

Thanks Pierre, that was the confusion, as when you pull the table from the ucsc website (from table browser), its somehow combines all the files and outputs them. So, finally I dumped all the tables individually using mysql and appended the output.

Cheers

ADD REPLY • link written 6.2 years ago by Sukhdeep Singh ♦ 9.5k

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