Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: Using Galaxy to sort SNPs according to their allele frequency
0
gravatar for adirsommer
6 months ago by
adirsommer • 0
adirsommer • 0 wrote:

Hi,

I have a list of SNPs uploaded to the Galaxy platform (https://usegalaxy.org/) and I'm looking to sort them according to their allele frequency. Can someone please guide me through the process?

Thank you.
snp galaxy • 200 views
ADD COMMENT • link •
modified 6 months ago by Jennifer Hillman Jackson ♦ 25k • written 6 months ago by adirsommer • 0
0
gravatar for Jennifer Hillman Jackson
6 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Are the SNPs in VCF format? The tools in the group NGS: VCF Manipulation can be used to summarize (count), filter on alleles, modify the formatting to be in a tabular format (aka "Tab-delimited") and many other operations.

VCF data is more useful in coordinate sorted format, not allele frequency when used with downstream tools, so there is no specific tool for that, however, those counts output in tabular format can be sorted with Filter and Sort > Sort data in ascending or descending order and used any way you want for custom queries/manipulations.

If this does not help, please explain your starting input format/source in more detail.

Galaxy tutorials, including the 101 that includes some basic text manipulation operations: https://galaxyproject.org/learn/

Thanks! Jen, Galaxy team
ADD COMMENT • link written 6 months ago by Jennifer Hillman Jackson ♦ 25k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 178 users visited in the last hour