The code is to get SNPs located in miRNA/pre-miRNA and their relationship(in loop, upstream of miRNA, downstream of miRNA, seed region or just in the miRNA) miRNA data is from mirBase while dbSNP data is from vcf file
Perl 100.00%
mirna-snp's Introduction
1) dbsnp135 vcf download at ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/v4.0/00-All.vcf.gz
something to make sure.
1) Is snp position in vcf file 0-based or 1-based
It is 1-based
2) Is pre-miRNA 1-based
yes
The code is to get SNPs located in miRNA/pre-miRNA and their relationship(in loop,
upstream of miRNA, downstream of miRNA, seed region or just in the miRNA)
miRNA data is from mirBase while dbSNP data is from vcf file