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Question: query using mysql on ucsc table browser
0
gravatar for bioguy24
4.2 years ago by
bioguy24 • 190
Chicago
bioguy24 • 190 wrote:

I have a folder of 57 text files each with 1000 locations in them.  I was going to use the mySQL browser at

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A

but I am getting a connection error using ubuntu 14.04

cmccabe@DTV-A5211QLM:~$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A
ERROR 2003 (HY000): Can't connect to MySQL server on 'genome-mysql.cse.ucsc.edu' (110)

Basically, I am trying to run a query in refGene that will use each of the locations in all 57 files and return the sequences of the CDS plus 10 bases at either end.

Example output:

>hg19_refGene_NM_001305275_0 range=chr1:955543-955763 5'pad=10 3'pad=10 strand=+ repeatMasking=none
cgcctgcgccATGGCCGGCCGGTCCCACCCGGGCCCGCTGCGGCCGCTGC
TGCCGCTCCTTGTGGTGGCCGCGTGCGTCCTGCCCGGAGCCGGCGGGACA
TGCCCGGAGCGCGCGCTGGAGCGGCGCGAGGAGGAGGCGAACGTGGTGCT
CACCGGGACGGTGGAGGAGATCCTCAACGTGGACCCGGTGCAGCACACGT
ACTCCTGCAAGgtgcgcccac
>hg19_refGene_NM_001305275_1 range=chr1:957571-957852 5'pad=10 3'pad=10 strand=+ repeatMasking=none
tccaccccagGTTCGGGTCTGGCGGTACTTGAAGGGCAAAGACCTGGTGG
CCCGGGAGAGCCTGCTGGACGGCGGCAACAAGGTGGTGATCAGCGGCTTT
GGAGACCCCCTCATCTGTGACAACCAGGTGTCCACTGGGGACACCAGGAT
CTTCTTTGTGAACCCTGCACCCCCATACCTGTGGCCAGCCCACAAGAACG
AGCTGATGCTCAACTCCAGCCTCATGCGGATCACCCTGCGGAACCTGGAG
GAGGTGGAGTTCTGTGTGGAAGgtgcgtggtg

I am not sure what is wrong or what query to use as AI have never used this tool.  Thank you :).
ucsc mysql next-gen sequence • 1.4k views
ADD COMMENT • link •
modified 4.2 years ago by Emily_Ensembl ♦ 20k • written 4.2 years ago by bioguy24 • 190
1

works for me.

$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg38 -e 'select now();
+---------------------+
| now()               |
+---------------------+
| 2016-01-19 09:29:40 |
+---------------------+

check your proxy settings?!!

ADD REPLY • link modified 3 months ago by RamRS ♦ 26k • written 4.2 years ago by Pierre Lindenbaum ♦ 127k
1

to get the fasta sequence: you're looking for tabix , or twoBitToFa see How To Get The Sequence Of A Genomic Region From Ucsc?

ADD REPLY • link written 4.2 years ago by Pierre Lindenbaum ♦ 127k

Looks like it is the proxy settings... thank you :).

ADD REPLY • link written 4.2 years ago by bioguy24 • 190
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