I have been asked to do differential and pathway analysis on some mouse RNAseq data.  I was provided with FASTQs, BAMs, and gene/transcript report tables from rsem.  The reads are 150 nt, paired-end from a MiSeq.  rsem was run against GRCm38 with Ensembl 74 annotations.  I'd like to reuse as much of the existing work as possible.

I have built some interactive volcano plots with ggvis and Shiny, and I'm starting to build a JBrowse site.

**A decent fraction** (10%?) of the genes with differential expression [Deseq2 adj p < 0.05, abs(log2fc) > 1] are **minimally annotated gene models like "GmNNN"** where the Ns are digits.

Some of those gene models have richer annotations in Ensembl 94, and some have been retired by 94.  I can use BLAST to manually show that some of the reads aligning to some of these models 
also align to other well-characterized genes, like protein or RNA components of ribosomes.

**Are there well-documented, web-based ways to automatically show other loci that the reads could have aligned to?**



Honestly, doing the analysis again seems to me the best. You can redo everything somewhat quickly with STAR+RSEM, or you could redo **very** quickly with Salmon or kallisto.