I'm new to Myrna and trying to figure out how I can use an aligner other than bowtie when executing Myrna. Is this even possible? If it is how would one do that?
background: I don't trust the current reference sequence for the species in which I have RNA-Seq data. I would like to construct a denovo transcriptome and would like to use Myrna to conduct the expression level analysis using my reference.
The problems I see is that I lose exon information, annotation become a problem (I believe I can use the establish reference and grab most of annotation), and I don't know what input Myrna needs if I skip the bowtie phase.
Any guidance would be appreciated
Joe
background: I don't trust the current reference sequence for the species in which I have RNA-Seq data. I would like to construct a denovo transcriptome and would like to use Myrna to conduct the expression level analysis using my reference.
The problems I see is that I lose exon information, annotation become a problem (I believe I can use the establish reference and grab most of annotation), and I don't know what input Myrna needs if I skip the bowtie phase.
Any guidance would be appreciated
Joe