I am analysing Ribo-Seq data (Illumina single end ~25 bp reads) using the Xtail pipeline. I also have RNA-Seq data sequenced using the same samples and sequencing chemistry (Illumina single end ~25 bp reads). During the bioinformatic analyses, we figured out that in around 48% of genes the Ribo-seq count is more than the RNA-Seq count for both treatment and control data. Strangely, there are also few genes (~3%) where we have ribo-seq reads but zero RNA-seq read count. Could anyone let me know if this is usual in such data analysis? However biologically this is somehow unbelievable to have Ribo-Seq of genes which are not transcribed (no RNA-Seq).
I used Xtail pipeline for data cleaning and analysis (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4822032/pdf/ncomms11194.pdf).
Many thanks in advance!