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.
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.