Kissplice2RefTranscriptome interpreting results

Question

[vguerracanedo]

Hi Everyone,

I was looking at my results from Kissplice2RefTranscriptome and I note that SNPs were annotated for my mitochondrial genes. This doesn't look right because the mitochondrial genes of my organism are haploid. I followed the steps as noted in the manual with a Trinity De novo assembly. Has anyone encountered this problem? is this a matter of adjusting the pipeline?

Best, Vanessa

[WouterDeCoster]

mitochondrial genes of my organism are haploid

Unless your organism is different than other eukaryotes your mitochondrial chromosome is all but haploid. It's massiveploid. I just invented that term, but it just means that you have many mitochondrial genomes in an average cell, which can definitely have SNPs.