Question: Extract sequences flanking SNPs from organism without reference genome
0
gravatar for konanamenanjacky
3.2 years ago by
konanamenanjacky0 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

blast snp • 922 views
ADD COMMENTlink modified 3.2 years ago by harold.smith.tarheel4.5k • written 3.2 years ago by konanamenanjacky0

Would you also have the GTF file? If so you could try the Variant Effect Predictor. You can annotate the variants if you have the fasta and the gtf. Check the help on cache and database.

ADD REPLYlink written 3.2 years ago by Denise - Open Targets5.0k

Thanks, No I don't have the GTF file.

ADD REPLYlink written 3.2 years ago by konanamenanjacky0

How was your VCF generated without a reference? Contig assembly then alignment? Alignment to related species reference?

ADD REPLYlink written 3.2 years ago by harold.smith.tarheel4.5k

Thank Harold, It is GBS, so DNA was digested with ApeKI and final libraries were sequenced using illumina. Alignement was done on partialy sequenced genome (made of contigs, so not annotated) of my species.

Thank a lot for your help

ADD REPLYlink written 3.2 years ago by konanamenanjacky0
2
gravatar for harold.smith.tarheel
3.2 years ago by
United States
harold.smith.tarheel4.5k wrote:

You can use BEDtools 'slop' to create a BED file of the flanking coordinates, then 'getfasta' to extract the sequences.

Note: this will require the refence contigs to which the reads were aligned.

ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by harold.smith.tarheel4.5k

Thanks a lot Harold, I will try and keep you informed!

ADD REPLYlink written 3.2 years ago by konanamenanjacky0

Thanks a lot Harold, It's works very well!

ADD REPLYlink written 3.2 years ago by konanamenanjacky0
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