I tried to retrieve a set of 20 bp length genomic sequences using
the UCSC Table Browser, using assembly track and providing a set of
The Table Browser returned large sequence regions that included the
requested regions instead of just the requested bases.
Is there a setting for UCSC Table Browser that will return just the
To extract genome sequence for specified coordinates you have (at
1) Use the Galaxy tool Fetch Sequences -> Extract Genomic DNA. Create
file of the coordinates (Interval or BED - see the tool for formatting
details). Be sure to set the target database. This will extract the
regions - and just those regions - directly into your history.
2) Create a custom track (BED file) of the coordinates, load it into
UCSC Genome Database as a custom track, bring it up in the UCSC Table
Browser (group = Custom track), make certain that region = genome, and
select output = fasta. Leave the rest of the settings at default,
including the box checked "Galaxy", to load back into your Galaxy main
The problem you encountered with the UCSC Table Browser is not really
problem, but is simply the way "regions" are interpreted for the query
function. When extracting coordinates from a track in the Table
the "regions" are used to extract overlapping regions from the target
track selected. It doesn't matter what the target track is - Assembly
(genome) or RefSeq genes (mRNA) - the same result type of result is
obtained -> the entire overlapping record from that track's primary
table. Useful, but not what you want for this particular query.
Try #1 and please let us know if you need more help!