What’s your problem? Open Thread
Welcome to the “What’s Your Problem?” (WYP) open thread. The purpose of this entry is to allow the community to ask questions on the use of genomics resources. Think of us as a virtual help desk. If you have a question about how to access a certain kind of data, or how to use a database, or what kind of resources there are for your particular research problem, just ask in the comments. OpenHelix staff will keep watch on the comment threads and answer those questions to the best of our knowledge. Additionally, we encourage readers to answer questions in the comments too. If you know the answer to another reader’s question, please chime in! The “WYP” thread will be posted every Thursday and remain at the top of the blog for 24 hours. Questions or problems asked on Thursday will be answered on Thursday to the best of our ability. You can leave questions on other days of the week, but the answer might not come that day.
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So What’s Your Problem? And What’s Your Solution? 
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Question:
If you have a list of a few hundred SNPs, say just 1/3 are on the array of interest, what’s the best way/fastest tool to find out if another SNP on your array might be tagging of these ungenotyped SNPs?
I use this sometimes: http://mather.well.ox.ac.uk/GLIDERS/, but the output is unfriendly.
Ideas?
You might want to use GVS, particularly BatchGVS (http://gvsbatch.gs.washington.edu/GVSBatch/). The interface and output are relatively straightforward. We’ve got a tutorial on GVS (free) here: http://www.openhelix.com/gvs Batch GVS allows you to put in a large number of SNPs.
You also might want to check out HaploView, a stand-alone (java) program that has a straightforward interface: http://www.broadinstitute.org/haploview/haploview-downloads
Or PLINK http://pngu.mgh.harvard.edu/~purcell/plink/ (gPLINK is a java tool for that)
Hi,
I’m looking into using dbEST to find support for some novel transcripts we have discovered experimentally, however I cannot find a simple way to download (in fasta or similar format) only human EST sequences from NCBI. Can you point me in the right direction?
Thanks,
Aaron
Hi Aaron–
That’s a good question. I actually hadn’t looked at the batch tools since the NCBI re-organization. You may be aware of the Entrez Utilities http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html and the Batch tools http://www.ncbi.nlm.nih.gov/sites/batchentrez?db=Nucleotide which might get you what you want.
But quite frankly, I would pull this out of UCSC (genome.ucsc.edu). The UCSC Human data contains data sets for mRNAs, ESTs, and spliced ESTs that would be helpful for you, I think. You could download these in batch from their Table Browser. Or you could use Galaxy (usegalaxy.org, and Get data from UCSC) as a handy interface to pull down large data sets like this and manipulate/process them.
There’s also another UCSC track for non-human ESTs (other ESTs is the title). And if I was looking at novel transcripts I’d be curious about other species too.
Does that help?