[Genome] extracting genomic regions from locations

[Hiram Clawson]

Good Morning Vesko:

See also:
http://genome.ucsc.edu/FAQ/FAQdownloads#download32

Format your data as a bed format:
http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED
you will have to add a dummy name and score column before your
strand.  Use the custom track input to the genome browser:
http://genome.ucsc.edu/goldenPath/help/customTrack.html
to load your locations into the genome browser.  Then
extract your sequence using the table browser:
http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#Sequence

See also, previous answers to this question in the mail list:
http://www.soe.ucsc.edu/pipermail/genome/2006-February/009864.html
http://www.soe.ucsc.edu/pipermail/genome/2007-May/013410.html
http://www.soe.ucsc.edu/pipermail/genome/2006-September/011647.html

--Hiram

Vesselin Baev wrote:
> Dear All,
>  how can I retrieve sequences from locations like this automatically:
> 
>  chr----start-----stop-----strand
>  9       108464802       108464823       -
>  11      110286355       110286377       +
>  14      101472070       101472091       +
>  14      101471691       101471712       +
>  14      101487793       101487815       +
>  7       137472049       137472068       +
>  X       49940888        49940909        +
> 
> 
>  Thanks!
>  Vesko
> 
>  ------------------------------------------------
>  Dr. Vesselin Baev
>  University of Plovdiv
>  Dept. Molecular Biology
>  Bioinformatics Group
>  Tzar Assen 24
>  Plovdiv 4000, BULGARIA
>  032/ 261 (534)
>  089/ 43 80 945
>  Skype: vesselin_baev
>  vebaev at gmail.com
>  baev at uni-plovdiv.bg