I am using MISO to quantify the expression level of individual isoforms annotated in ENSEMBL GRCh37.65. I want to highlight that I am NOT quantifying only the region covering alternative splicing event, rather the full length isoform. The input GFF file contains annotation of genes encoding single or multiple isoforms.
I am facing issues with single isoform genes. I found in the output file that MISO calculates read counts for two isoforms for those cases where there is only one isoform annotated in my GFF file. Furthermore, it also compares read counts for two isoforms. I am not able to understand how it calculates the read counts for the second isoform of a gene which does not exist.
Below is the read count (in MISO format) of a single isoform gene:
I will highly appreciate if some one can help me out understanding this problem.