I have fastq files from WGS done on a transgenic mouse model using an Illumina platform. The transgenic construct consists of an unknown lox-stop-lox sequence, the native copy of our gene of interest (which is an intron-less gene natively located on chromosome 13), an unknown IRES sequence, and an unknown EGFP sequence. The mouse was sourced from another lab, and we have not been able to determine the sequence of the EGFP region of the sequence, which has complicated downstream single-cell RNA sequencing analysis using 3' chemistry. We know the gene was inserted at the Rosa26 locus on chromosome 6. Since the insertion location and the sequence of the insertion location are known, how would I go about getting the sequence of this unknown gene or, at the very least, the 3' end containing EGFP? I have an assembly made using ABySS, but there are over 120k contigs, so I'm rerunning ABySS using different values of k in an attempt to bring that down.
I apologize if this is a basic question; I'm very new to working with WGS data.
