Hi every one. I got stuck in my NGS project and was wondering if someone can advise me.
I have downloaded Illumina paired-end reads of the whole genome of several M. tuberculosis strains from ENA database. I have a gene of 1800bp length (gene X) from M. tuberculosis. I want to investigate the SNPs variation of gene X among different strains of M. tuberculosis.
After evaluating the read quality, and trimming the reads, is it ok to map illumina DNA-seq reads against one single gene? According to the literature, all the reads are mapped against the whole genome (ref genome), and not a single gene while based on my project, I have to map the whole genome to a single gene! Any suggestion is greatly appreciated.