How to correctly map CORALL-generated RNA-seq data to a reference genome?
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!
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niklasjoshua.ebner •
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