Question: Extracting reads from SNP list
gravatar for d.angra
3.4 years ago by
United Kingdom
d.angra50 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



snp • 956 views
ADD COMMENTlink modified 3.4 years ago by Jennifer Hillman Jackson25k • written 3.4 years ago by d.angra50
gravatar for Jennifer Hillman Jackson
3.4 years ago by
United States
Jennifer Hillman Jackson25k wrote:


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 COMMENTlink written 3.4 years ago by Jennifer Hillman Jackson25k
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