Hi Biostars,

I am working on a project which involves paried end RNA-bulk sequencing data. When I look through my list of DEGs, then I see that the gene IL3RA has a p-adj value < 0.05, and a log2FC value = 3.88. For this experiment it is expected that IL3RA is upregulated, however when I dig further into the DEG list, then I find LOC genes as well, and especially LOC101928032 is very interesting because it is located on the opposite DNA-string of IL3RA within the same window. The log2FC value of LOC101928032 is 2.92

My question is; am I loosing read counts from IL3RA because it goes to LOC101928032? My concern is if IL3RA actually have a higher log2FC than 3.88, but is lost because LOC101928032 is included in the sequencing alignment?

Find out if your library protocol is stranded or not. If standed then these two genes should be independent. If not stranded then they should have similar counts for the intersecting exons. In this screenshot I see that roughly three exons share some sequence content.

Its also worth eyeballing the reads in the BAM files directly with IGV to find out exactly whats going on.