Question: Galaxy Query
0
Whiteley, Gareth • 10 wrote:
Hello,
If I was to choose the following search criteria Group:all tracks,
track:SNP, region: chr5:7922217-7954237, then click INTERSECT and
choose Group:all tracks, track:TFBS conserved and select GTF output
format. This example searches for any SNPs that are in the
Transcription factor binding sites within the genomic region that
codes for the MTRR gene, but the output does not tell me that the SNP
rs6868871 is found in the TFBS V$58_01 914, I have to work that out
for myself by then searching the whole table again but from a TFBS
start point and intersecting with SNPs.
I am trying to use galaxy to Join two Queries side by side on a
specified field. I am trying to relate SNPs to the TFBS they are
associated with. For example, SNP rs6868871 is found in TFBS V$58_01
914. However, i can not seem to get galaxy to work, i think this is
because the SNP site is something like this '165878639 - 165878640'
and a TFBS site is something like this '165878630 - 165878641' and
although the positions overlap, galaxy can not tell that. Is this the
case? Or do you know of how i can get around it?
Regards,
Gareth Whiteley
Gareth Whiteley
University of Liverpool
Department of Pharmacology and Therapeutics
The Sherrington Buildings
Ashton Street
Liverpool L69 7GE
Tel: 0151 795 4224
E-mail: g.whiteley@liverpool.ac.uk
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modified 9.2 years ago
by
Anton Nekrutenko ♦ 1.7k
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written
10.5 years ago by
Whiteley, Gareth • 10
