I have a general question/issue I wonder if anyone knows a solution to. Firstly, as I said in a previous message, i was pleased with the integration of built-in annotation files (mm10, Hg19 etc) in featureCounts on Galaxy main. I am now analyzing Rat genome data (rn6 build). The data looks good on conversion to BigWig and corresponds (on the whole) well with the FeatureCounts output. However, I did notice a couple of well annotated mRNAs that although giving clear signals looking at the BigWig genome alignments, fail to give representative counts under featurecounts. The annotation and exon locations etc. look fine in the GTF file I use for the analysis and as I said the BigWig clearly shows high signal counts for the exons, so the mapping is ok. Other genes, upon random selection, check out fine, so like I say its just the odd gene every now and again that seems to get miss-counted. I probably wouldn't have even noticed if it wasn't for the fact that one of the genes I checked was a key gene for our research. Ideas ?