I have a fastq file generated from a whole genome sequencing by C. elegans samples and I want to find in which site (or sites) a construct/plasmid has been integrated in the genome, comparing my sequence with a published genome in Ensembl (WB235).
I had a C. elegans strain with a construct integrated in the genome. From the construct design, I expect it to integrate into chromosome III of C. Elegans. So, by using a tipical SNPs and indels workflow from Varscan, I managed to identify Variants in all samples. Furthermore, I also analyzed the CNVs through BreakDance tool only in chr III.
But my question is: How can I find where the construct is integrated? I would like the position (Start and End) respect to a genome reference. It's possible?
Thanks for all.