Mapping SNP isomiRs to rs IDs

[mshadbolt]

Hi there

Thanks for the great package.

I was wondering if there is a way to map back isomiRs with known SNPs to their respective rsIDs or other variant nomenclature/genomic coordinate?

For example I ran the pipeline and got hits against 3 SNP isomiRs in hsa-mir-1304

"hsa-miR-1304-3p.SNPA" "hsa-miR-1304-3p.SNPC" "hsa-miR-1304-5p.SNPC"

Does the pipeline only include SNPs in > 1% of the population? For example for hsa-miR-1304-3p the very common SNP is rs2155248 with alleles A and C, so the fact that I detected SNPA and SNPC in this sample would mean I most likely have a heterozygous individual with this SNP?

Thanks in advance for the clarification.

[luketerry]

The SNP information from different species are downloaded from the miRNASNP V2.0 database. You could access it by http://bioinfo.life.hust.edu.cn/miRNASNP2/download.php Here what I need to correct is that miRge includes SNPs in > 0.1% of the population for human. As for your example, .SNPC means the canonical miRNA sequence and .SNPA, *SNPB... means miRNAs with SNP. If you detected SNPA and SNPC in one sample, you need to check the location of mutated nucleotide of the reads. If it happens at the SNP position, this is likely to be a heterozygous individual with this SNP.