[Genome] problems in loading repeat masker to mysql

[fungazid fungazid]

Archana Hi,
   
  The rmsk tables from http://genome-test.cse.ucsc.edu/ were loaded successfully into my mysql, as suggested by your engineers. So now everything is OK. 
   
  Thank you :),
  Avi
   
  
Archana Thakkapallayil <archanat at soe.ucsc.edu> wrote:
  Hello Avi,

Here is a response from one of our engineers:

The .out files are in a slightly different format from our database 
tables and dump .txt files. If you are going to work directly with 
mysql, you should use the .sql/.txt files. We provide .out for those who 
are used to working directly with RepeatMasker output files.

Unfortunately, there is no database dump for the rabbit database. The 
.sql file for rmsk can be found in the Annotation database dump for a 
different assembly e.g., 
http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/

You could download the chr1_rmsk.sql from here and then rename this for 
use with the rabbit genome.

You can then obtain the data directly from the 'Table Browser' on our 
test server at:

http://genome-test.cse.ucsc.edu/

The table that contains this information is called 'rmsk', which comes 
under group : Variation and Repeats, and track: Repeatmasker.

Information on using the Table Browser is here:
http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html

Another suggestion is that you need to add LOCAL to your MySQL command:

"LOAD DATA LOCAL INFILE"

I hope this information helps. Let us know if you run into any problems.

Regards,

Archana
UCSC Genome Bioinformatics Group



fungazid fungazid wrote:
> Hello world,
> 
> Please help me, I have a problem in loading rmsk.out file for oryCun1 and loxAfr1 builds into mysql. I tried to load it with LOAD DATA INFILE command with no success. It seems that LOAD DATA INFILE can't handle the spacing between Fields.
> I got the files from FTP hgdownload.cse.ucsc.edu
> 
> many thaks
> Avi
>
> 
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