I have some PacBio RNA-seq data that should have a jumbled gene in it (e.g. the exons are not in the canonical order but instead go something like 1, 2, 3, 5, 6, 4, 5, 7, 8 etc - scrambled exons). I thought that by mapping my FASTQ with HISAT2 followed by mapping the resulting .bam to the reference GTF that I would see this jumbling event in the resulting GTF for my BAM - but nothing - the codes are all "=" for this gene when I do a GFFCompare. If I open the BAM in IGV I see the jumbling event, but what I'm looking for is a way of find other jumbling events that I don't already know about. Any suggestions?
Question: Identify jumbled transcripts (scrambled exons) using HISAT2, stringtie, and GFFcompare?
11 months ago by
wolfgang.rumpf • 10
wolfgang.rumpf • 10 wrote:
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