I'm pretty novice when it comes to bioinformatics. I am currently working on a project where I am trying to call SNPs from frog species which have not been completely sequenced. I have RNA from 10 different tissues among 5 closely related frog species.
I've tried aligning these sequences to a reference genome of a more distantly related frog that has been completely sequenced but the results are very poor (2-3% of the reads are mapped to the reference genome).
I thought perhaps I may be able to do a de novo assembly of the RNA sequences of each tissue and use the resulting contigs as a "reference genome" for the alignment.
Does anyone have any experience with this? Is this a reasonable way to call SNPs from data without a reference genome?