I am attempting to use galaxy to calculate the percentage of a nucleotide at a specific position within MiSeq data. Any suggestions on a proper workflow? For context I am looking at low abundance RNA editing at a specific position within an amplicon.
My first attempt was using snippy and a FASTA of our reference. This was successful in identifying our SNP in a VCF file but I’m not sure how to get from here to a percent abundance?
Very new to this, so I apologize. It’s possible I’m way off-base or have worded this question poorly. Any suggestions are much appreciated!