Question: Galaxy Query
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gravatar for Whiteley, Gareth
10.1 years ago by
Whiteley, Gareth10 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
galaxy • 752 views
ADD COMMENTlink modified 8.8 years ago by Anton Nekrutenko1.7k • written 10.1 years ago by Whiteley, Gareth10
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gravatar for Anton Nekrutenko
10.1 years ago by
Penn State
Anton Nekrutenko1.7k wrote:
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 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
ADD COMMENTlink written 10.1 years ago by Anton Nekrutenko1.7k
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gravatar for Anton Nekrutenko
10.0 years ago by
Penn State
Anton Nekrutenko1.7k wrote:
Gareth: Sorry for the delay. There are two way of dealing with this. I attached a link to a screencast that highlights the two approaches. In the first, you must upload datasets into galaxy and simply run the join tool. The second approach is to use a new galaxy tool called "Annotation profiler". It allows you to compare your set of genomic features against the entire UCSC database in a single pass (at this point it can only be used against hg18 annotations). Try it out and let us know if you have any further questions. The movie is here: http://screencast.g2.bx.psu.edu/SNPs_TFBS.mov anton 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
ADD COMMENTlink written 10.0 years ago by Anton Nekrutenko1.7k
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gravatar for Anton Nekrutenko
8.8 years ago by
Penn State
Anton Nekrutenko1.7k wrote:
Gerome: This question is more applicable to our galaxy-user list, so I am redirecting it there. See the reply below. What you are trying to do is, in fact, quite easy to perform with galaxy: 1. Extend gene coordinates either direction with "Operate of Genomic Intervals->Get Flanks" 2. Join the newly extended genes with SNP dataset using "Operate of Genomic Intervals->Join" 3. Group by gene name and concatenate on SNP name using "Join, Subtract and Group -> Join". Please, see this history: http://main.g2.bx.psu.edu/history/imp?id=354aae8cd0d5e1c5 for an example. If you click on "rerun" link within history item (see attached image), you will be able to see parameters I've used. NOTE: There are two kind of join in Galaxy: relational join ("Join, Subtract and Group->Join") and interval join ("Operate of Genomic Intervals->Join"). Here we use interval join. If have any trouble I will make a galactic quickie (short movie) for you. Thanks, anton galaxy team
ADD COMMENTlink written 8.8 years ago by Anton Nekrutenko1.7k
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