Forum: How to find the distance from one variant to 5' UTR and 3' UTR
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3.9 years ago by
89759864490
China
89759864490 wrote:

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!

snp sequence forum gene genome • 1.0k views
ADD COMMENTlink modified 3.9 years ago by ivivek_ngs4.9k • written 3.9 years ago by 89759864490
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3.9 years ago by
ivivek_ngs4.9k
Seattle,WA, USA
ivivek_ngs4.9k wrote:

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.

VEP

VAAST

snpEFF

ANNOVAR

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

ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by ivivek_ngs4.9k
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