Strandedness during cDNA synthesis, the stranded parameter in Htseq-Count and analysis of RNA-Seq aata

Krishna A Srinivasan, Suman K Virdee, Andrew G McArthur

Brief Funct Genomics 2020 May 16 [Epub ahead of print]

RNA sequencing (RNA-Seq) is a complicated protocol, both in the laboratory in generation of data and at the computer in analysis of results. Several decisions during RNA-Seq library construction have important implications for analysis, most notably strandedness during complementary DNA library construction. Here, we clarify bioinformatic decisions related to strandedness in both alignment of DNA sequencing reads to reference genomes and subsequent determination of transcript abundance.

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