I completed a WGS alignment using 150PE fastq reads via BowTie2 to a locally installed plant genome. The alignment worked well, and I am able to visualize the reads by Integrated Genome Viewer (IGV). However at my site of interest, I see that I have a large set of paired reads where the pair is not mapped. I am thinking that I have a non-reference sequence insertion at that site that is not tolerated by BowTie2 and is discarded during sequence processing, and there doesn’t seem to be an intuitive way to find my discarded reads of interest.
Is anyone aware of workflows on Galaxy that may tolerate non-genomic sequences better? Maybe de novo genome assembly workflows that can handle large genomes (400Mbp)? Apologies in advance if this is not a Galaxy question, but is instead one for a more bioinformatically-oriented forum.