Entering edit mode
3.0 years ago
Hello Biostars,
I have a general question regarding data from an RNA-seq experiment. The stranded, paired-end data were generated using Lexogen's CORALL Total RNA-Seq kit, and the manual states that "Read 1 reflects the RNA transcript and not the cDNA". When I map the data against the genome of my species using tophat I get low mapping rates for the left reads (0.6%) but good mapping rates for the right reads. What are the correct steps I need to take with these kinds of data? Am I missing something obvious? The ultimate goal would be differential expression analysis.
Thank you!
