Excuse me,
I want to know how many bases there are from one variant to 5' UTR and 3' UTR. Are there any step-by-step instructions about how to finish that job in UCSC genome browser?
Many thanks in advance!
Do you wish to know if your variant is in 5' or 3' UTR? in that case you have annotate your SNP or lets say SNV file with any tools like VEP , snpEFF , ANNOVAR, VAAST and then see where your variants are at corresponding annotated loci's, if you wish to see that then in a browser you need to upload the vcf file of the SNVs along with its index file for the correct assembly in UCSC or IGV to see the variants , also charge the alignment file to see the read mappings if you want.
In that case you can always download the bed regions for each 5' and 3' UTR and then calculate the distances with any standard tool.
You can download all the regions of 3' and 5' and intersect them with your SNV as well and then try to compute the distance based on the length of the UTRs
Alternately take a look at these discussions here
You can also you R genomicfeatures to the trick as well
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
version 2.3.6