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Question: Extracting reads from SNP list
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gravatar for d.angra
3.4 years ago by
d.angra • 50
United Kingdom
d.angra • 50 wrote:

Hi Galaxy experts

I am working on a non-model species and have created a denovo transcriptome assembly from more than 10 datasets, in order to identify SNPs. I have used galaxy to successfully obtain a list of good quality, high confidence SNPs. Now I need to extract the reads from the SNP list. Can any of you please advice me on tools to use in galaxy to help me achieve this?

 

Thanks in advance

 

Viva
snp • 956 views
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modified 3.4 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.4 years ago by d.angra • 50
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gravatar for Jennifer Hillman Jackson
3.4 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

One tool to use is "vcf2fasta" from the Vcftools suite. This tool is under active development and will be available shortly in the Tool Shed for use in Galaxy. 

The alternative for now is to obtain coordinates from VCF files, pad out the ranges, create your own BED file, then extract from the genomic. However, this will not have the SNP content included unless it also happened to be in the reference genome (a few usually are). 

Thanks for using Galaxy, Jen, Galaxy team
ADD COMMENT • link written 3.4 years ago by Jennifer Hillman Jackson ♦ 25k
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