I am helping to analyze some RNA sequencing data from exosome content and I would appreciate any advice or pointers.
Briefly, the exosomes were precipitated from serum using SBI reagents. Total RNA was extracted for 150 paired end and unstranded library construction. We have good sequencing depth (> 30 million reads) and good mapping rates (> 80% mapped to genome using STAR aligner on standard igenomes). However, the number of reads assigned to a transcript is extremely low (<10%) with a high proportion mapping to introns or intergenic regions. This seems to mirror what has been reported previously (e.g. Page 13 of https://www.systembio.com/wp-content/uploads/SBI-Brochure-Exosome-Research-Products-and-Services.pdf; https://www.ncbi.nlm.nih.gov/pubmed/29282313).
I would appreciate for advice/reference on how to characterize the different transcript biotypes proportions (mRNA antisense, antisense RNAs, processed transcript RNAs, lncRNA, rRNA). Also, on how to proceed with differential expression analysis. Thank you.
Adaikalavan Ramasamy :: Senior Research Scientist :: Computational Genomics :: Genome Institute of Singapore :: Agency for Science, Technology and Research (A*STAR) 60 Biopolis Street, #02-01 Genome :: Singapore 138672 :: DID: +65 6808 8141 :: Email: firstname.lastname@example.org