You can do all the intersects within Galaxy. If I understand
correctly you are trying to intersect conserved TFBPs with SNPs? Right?
Let me know and will send you a detailed step-by-step demo.
On Jun 5, 2008, at 8:02 AM, Whiteley, Gareth wrote:
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?
University of Liverpool
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Department of Biochemistry and Molecular Biology
Center for Comparative Genomics and Bioinformatics
Penn State University