Gareth: 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. anton galaxy team On Jun 5, 2008, at 8:02 AM, Whiteley, Gareth 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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Anton Nekrutenko Asst. Professor Department of Biochemistry and Molecular Biology Center for Comparative Genomics and Bioinformatics Penn State University anton@bx.psu.edu http://nekrut.bx.psu.edu 814.865.4752