My idea is to align whole-genome sequencing data (as fastq files after, 30× coverage, gDNA) to the reference mouse genome (NCBI), extract the immunoglobulin locus and compare it to the reference. I think the question is too broad but maybe a hint how to start ? (I'm new to the field.)
Task is: to check for difference between reference genome and a sample for 100-200 genes.
I checked these: question (but it's closed), answer (gave a hint about whole reference mapping not only the locus of interest), question (not answered), question (useful I guess but not sure).
Additional info:
Instrument Platform: ILLUMINA
Instrument Model: HiSeq X Ten
Library Layout: PAIRED
Library Strategy: WGS
Library Source: GENOMIC
Typical sequence length distribution from FastQC: 150nt.
I have Win10 with WSL 1 installed.