Friday, 9 September 2011

I am not a Bioinformatician: 1. Experiences with UCSC DAS

I am not a Bioinformatician but I often want to do things Bioinformaticians say are easy. This is the first in a possible series of blogs about my experiences with Bioinformatics, text mining, etc. I'd be very happy to receive comments on the approaches I try or hints on how to do what I am trying to do more easily. For now I am not learning to program or run scripts from a command line. I am happy to try something in Galaxy.
Part of the reason for these posts is so I can remeber how to do this next time myself.
This is meant to be the non-Bioinformaticians way of doing things!

I used to just send an email to one of the Bioinformaticians at work but I couldn't help but take the hint that they had work to do as well. So now I'll usually try to find out if I can do what I want myself with publically available, usually web-based tools. I figure that even if I don't succeed my trying is evidence I'm not just abusing their better experience. It also helps me better explain what I want so they don't do some work for me and then I say how nice it is but it is not really what I thought I wanted after all.  


UCSC Distributed Annotation Service (DAS):
 The "DAS" server allows you to download data directly from UCSC. I suspect it is built to be queried from under the hood rather than through a URL. However it is an easy way to get the sequence from genomic coordinates so I like it.

There is a simple FAQ here. And a query for a sequnce looks like this http://genome.ucsc.edu/cgi-bin/das/hg18/dna?segment=chr2:51409549,51409749 which will return 200bp of sequence from chr2 in Hg19 build of the Human genome.

Here's how I used DAS and other tools to design some primers from a SNP:

Designing PCR primers from an dbSNP rsID: I am hoping to design some PCR assays to look at regions around SNPs. I got a list of SNPs from a colleague wth lots of information about them position, alleles, MAF, etc. However I wanted to take this list and design PCR primers to all 24 SNPs as quickly as possible. 
Getting SNP locations: I was already sent the locations along with rsID's but I wanted to see if I could find them myself. I like UCSC and it is usually my first port of call when looking for sequence information. In this case I simply entered an rsID into the UCSC position/search box (Image:UCSC RsID search) and then clicked through the link (Image: UCSC rsID results). This gives me the all important location information, chr1:4181020-4181020 in the case of rs10799216. 
Getting flanking sequence: I  used Excel (not a bioinformaticians favourite tool) to create a UCSC DAS address (Image: Excel to create DAS address) to pull out the flanking regions 100bp either side of the SNP (Image: UCSC DAS results). 
Designing suitable primers: I used the sequence results from the DAS query in Primer3 (image: Primer3 Input) wth the parameters Targets=100,2 (primers surronding the 2 bases at position 100), ProdcutSizeRange=30-75 (I want short products) and NumberToReturn=50 (50 sets of primers). Hey presto PCR primers (Image: Primer3 Output)

Now I can get on and order some primers to test in the lab, where I feel much more in my conmfort zone.




UCSC rsID search



















UCSC rsID results



















Excel to create DAS address

















UCSC DAS results



















Primer3 Input



















Primer3 Output



















SNAP from the Broad


















SNAP query



















SNAP results
 













about the snp data and using excel and word to generate a DAS list and get data fast even though I'm not a bioinformaticiain!!!

1 comment:

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