> For the complete documentation index, see [llms.txt](https://igb.mit.edu/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://igb.mit.edu/bioinformatics-topics/tasks-bioinformatics-methods/ucsc-genome-bioinformatics/galaxy/galaxy-snp-interval-data.md).
# Galaxy SNP Interval Data
his example is inspired by a screencast published on the Galaxy website. It consists in combining exon information and SNP information, both represented as interval data.
**1. Load exon data from UCSC tables**
* On the Tool Panel, click on Get Data → UCSC Main Table Browser.
* This tools allows you to upload data from the UCSC Tables.
* Use the following parameters:
* Group: Variation and Repeats
* Track: SNP(130)
* Region: chr19:1-100,000
* Output format: BED
* Send output to Galaxy: checked
* Click "Get Output" button.
* Select the radiobox so that one BED record is created for the whole gene.
* Click the button "send query to Galaxy"
* With these parameters, this tool creates a BED file containing all the SNPs for the first 1M bases of chromosome 19.
* Once the job is completed, change the name of the dataset to "SNPs chr19".
**2. Load SNP data from UCSC tables**
* On the Tool Panel, click on Get Data → UCSC Main Table Browser.
* This tools allows you to upload data from the UCSC Tables.
* Use the following parameters:
* Group: Genes and Gene Prediction
* Track: UCSC Genes
* Region: chr19:1-100,000
* Output format: BED
* Send output to Galaxy: checked
* Click "Get Output" button.
* Select the radiobox so that one BED record is created per coding exon.
* Click the button "send query to Galaxy"
* With these parameters, this tool creates a BED file containing all the exon information for the first 1M bases of chromosome 19.
* Once the job is completed, change the name of the dataset to "exons chr19".
**3. Join exon and SNP information**
* On the Tool Panel, click on Operate on Genomic Intervals → Join the intervals.
* This tools allows you to join the information from two interval files based on the coordinates of each feature.
* Select the SNP chr19 and the exons chr19 files as input.
* Click on the "Execute" button.
* Because some exons might contain multiple SNPs, the resulting output might have size greater than the two input files.
**4. Find the number of SNPs per exon**
* On the Tool Panel, click on Join, Subtract and Group → Group.
* This tools groups the information based on a given column and performs the aggregation operations on the other columns.
* Select data 3 as input.
* Select column 4 (exon ID).
* Add operation to count c4.
* Click on the "Execute" button.
**5. Find the exon with the most SNPs**
* On the Tool Panel, click on Filter and Sort → Sort.
* This tools ...
* Select data 4 as input.
* Select column 2 as sorting key.
* Click on the "Execute" button.
**6. Find how many chromosomes have a given number of exons**
* On the Tool Panel, click on Join, Subtract, Group → Group.
* This tools ...
* Select data 5 as input (sorted).
* Select column 2 as sorting key.
* Set the operation to "count" on column 1.
* Click on the "Execute" button.
**7. Filter exons with at least 10 SNPs**
* On the Tool Panel, click on Filter and Sort → Filter.
* This tools ...
* Select data 5 as input (sorted).
* Set the condition to SNP count greater than 10 (i.e. c2 >= 10).
* Click on the "Execute" button.
**8. Retrieve original information for exons**
* On the Tool Panel, click on Join, Subtract, Group → Join.
* This tools ...
* This is equivalent to a relational join (not an interval join).
* Select the exons with more than 10 SNPs as first input.
* Select the exon data for chr19:1-1,000,000 as second input.
* Select column 1 (exonID) for the first file.
* Select column 4 (exonID) for the second file.
* Click the "Execute" button.
* Now repeat this step but invert the order of the file. Note that this time the output is a BED-formatted output, wherease before it was a tabular file.
**9. Display using the UCSC Browser**
* On the Data Panel on the right-hand size, click on the last job → Display at UCSC.
* The User track show the exons that have more than 10 SNPs in the region of chr19 considered.
