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3.6 years ago
bagheri
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0
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.
Yes, you will need to map reads to the whole genome (or exome or other targeted panel) - this is determined by the sequencing library source for the reads. You've downloaded Whole Genome Sequencing data, so you'll need to align to the entire genome. Anything else would be inaccurate. Once you align the reads and call variants, you can zero in on your gene of interest for further downstream analysis.
@RamRS Many thanks for your response. I will follow your advice and will map all the reads against the ref genome, and call the SNPs. How can i zero in on my gene of interest?
Annotate your VCF with VEP (or extract the gene region from the VCF and annotate just that). That will give you all the information you need.
Cannot thank you enough man!