Entering edit mode
9.9 years ago
hpapoli
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150
Hello,
I am going to prepare a set of SNPs for genotyping by GoldenGateAssay.
The format of the file required is as follows:
SNPname1 ..............ATWCCCAT[C/T]GCCTATTGG..................
And it has been indicated that any SNP in the flanking sequence should be coded by the IUPAC ambiguity codes.
I have a file with a set of my SNPs and I am going to extract the sequences from my FASTA file using the following command in bedtools:
bedtools slop [OPTIONS] -i <BED/GFF/VCF> -g <GENOME> [-b or (-l and -r)]
However, two things remain unclear to me:
- How should I turn any SNP in the flanking region into an IUPAC code?
- How should I specify the SNP position like [C/T]?
I was wondering if there is any available tools for this purpose or I should go on trying to develop my own scripts for that.
Thanks in advance
Hi hpapoli,
I also need to do the task as you describe above. If you got that working could you please share the script/solution for extracting sequences around target SNPs and also adding IUPAC codes for the SNPs in the flanking regions.
Regards
SS