I'm trying to identify snp in a gene. But when I was looking for information about it / software for snp calling, mostly the ones I saw involve snp in genome sequence instead of only involving a specific gene. So can someone give some advice on how can I identify snp of a gene?
To expand on the comment by Ram first and foremost the type of data that you have determines the process by which you can establish a SNP.
If you have genome-wide high throughput data, then your methods will have to be genome-wide alignment, then variant-calling followed by identifying the coding regions of the gene of interest and then looking for SNPs in those regions.
If you have single long sequences specific to one gene, then you would perform a pairwise alignment between your data and the reference, then use the results of that to directly identify mismatching bases as SNPs.
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I assume you're looking for a single nucleotide variant that falls in a gene locus. If you have an alignment file, you can look at the read pileup across the gene to pick loci where the sample differs from the reference genome. To call variants, you will need to use a variant calling tool, which usually operate on the whole exome/genome. It should technically be possible to call variants in just a gene (as a gene is a subset of the genome much like an exome is a subset of the genome). However, you will need the alignment file that covers the entire exome/genome as restricting alignments can lead to high false positives.
Yes Im trying to look for single nucleotide variant in a gene locus. The gene was actually identified/ obtained from my assembled genome and currently I'm trying to further analyse the differences in my gene from the reference gene (which leads to SNP identification). You've mentioned that I'll still require to have the alignment file that covers the entire genome, does this means I'll still need to use my assembled genome for snp calling instead of only using my gene sequence to identify my single nucleotide variant?
Your gene is from your assembled genome (I'm assuming you mean you aligned reads to a reference to get this assembled genome. Please let me know if that's not the case) - so you will need to use a variant caller on the assembly/alignment and then narrow the results to the gene of interest.
(My assembled genome is through de novo assembly.) So I'll still have to do genome-wide SNP identification only after that I filter out the others and focus on my gene only is it right?