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Question: Extract SNPs flanking sequence from organisme without reference genome
1
gravatar for Konan
2.2 years ago by
Konan • 20
France/Montpellier
Konan • 20 wrote:

Hi, I'm new in managing DNA sequences and I'm looking for help. I have fastq and vcf files from the sequencing of my samples. The plant species on which I work (Lagenaria siceraria) has no reference genome. What I want to do is to extract SNPs flanking sequences and make a blast in Plant RefSeq for determining the putative functions of my SNPs. All the posts Ive read are related to species that have model organism. Then, could someone help me please?

Thanks
de-novo extract-sequence snp reference-data • 950 views
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modified 2.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.2 years ago by Konan • 20
1
gravatar for Jennifer Hillman Jackson
2.2 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Some form of an assembled reference fasta file will be needed to perform this function. This can be a transcriptome or genome assembly (complete or partial, for either) - with the sequences mapped to that assembled fasta file. Use a Custom reference genome/build when working with your own assembly.

Help:

Recent publication that outlines computational approaches when performing de-novo variant analysis. This may be a fit for your analysis, or portions of it may be helpful. A Galaxy tutorial/example is included: http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1039-4

Thanks, Jen, Galaxy team
ADD COMMENT • link written 2.2 years ago by Jennifer Hillman Jackson ♦ 25k
1

Thanks a lot Jen, I will follow your Avice and let keep you informed!

ADD REPLY • link written 2.2 years ago by Konan • 20
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