PAM50 subtyping RNA-Seq nested gene

Question

[rpraveenkumarbio]

Planning to do breast cancer subtyping based on PAM50 model using RNA-Seq data. https://www.bioconductor.org/packages/release/bioc/html/genefu.html

The conundrum I am facing is that one of the 'PAM50' gene “MIA” is annotated as nested in "ensembl-84. The annotation is that "MIA" is nested in a long gene “MIA-RAB4B”. Hence all the reads mapped to MIA are regarded ambiguous. This is like the last case in the HTSeq example here http://www-huber.embl.de/users/anders/HTSeq/doc/count.html.

Any suggestions are welcome. Should you suggest me to go with Data (no MIA counts) as it is or get-rid of long gene “MIA-RAB4B” in the annotation file to get MIA counts for the sake of subtyping.