I recently had some Iso-Seq sequencing done on my organism catfish on the new Sequel platform and got weird alignments for a size selected 4 Kilobase and up fraction after running the isoseq3 pipeline. When I investigated the exon intron junctions using data from (Pac Bio Iso-Seq, Illumina RNA-seq) against our private reference genome, I get PacBio Iso-Seq reads where the sequence length is greater than the seq length on the reference for my bam alignments:
Seq length: 6751
Seq length on ref: 5267
When blasting the sequence in NCBI it shows 5% similarity to the publicly-available genome. I'll attach a JBrowse image with the same RNA sequenced with Illumina paired RNA-seq. I also included a image and circled the pacbio contig and Illumina is above.
Is this a problem with JBrowse?
Does this mean that some DNA was sequenced with the catfish cDNA?
Why is this aligned sequence's length longer than the length of the reference genome region to which it is aligned?