Hello and merry Christmas
I having trouble for doing an small RNA-seq analyzing So, i align my data with rRNA reference which i downloaded from BioMART.(with Bowtie2) and then took the unaligned reads and map them to my hairpin reference which i downloaded from MirBase(with Bowtie2) and finally get the counts with featureCount(enabled to do not discard multimappers). but at the end i have zero count for DEG step. what should i do ?