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Question: Counting number of times multiple defined values appear in the dataset
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gravatar for aparker14
16 months ago by
aparker14 • 10
aparker14 • 10 wrote:

I have gotten SNP data on a number of regions via UCSC genome browser. I have assigned all SNPs within a region to a unique identifier (eg 001, 002 etc) using a dataset of my own and using the join on genomic intervals tool. However, I now wish to know how many SNPs belong to each unique identifier. How might I go about doing this?
galaxy • 367 views
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modified 16 months ago by Guy Reeves • 1.0k • written 16 months ago by aparker14 • 10
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gravatar for Guy Reeves
16 months ago by
Guy Reeves • 1.0k
Germany
Guy Reeves • 1.0k wrote:

If you want to count the number of variants in genes then SNPeff. gives such a report for genes. This will be possible on usegalaxy.org if you are working with a reference genomes which is already present as a drop down option.
What you want to do seams easy but I cannot think of another way off the top of my head. say if you found another way. Cheers

Guy
ADD COMMENT • link written 16 months ago by Guy Reeves • 1.0k
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