Preprint Article Version 1 This version is not peer-reviewed

Strandedness During cDNA Synthesis, the Stranded Parameter in htseq-count, and Analysis of RNA-Seq Data

Version 1 : Received: 8 March 2019 / Approved: 11 March 2019 / Online: 11 March 2019 (09:06:40 CET)

How to cite: Srinivasan, K.; Virdee, S.; McArthur, A. Strandedness During cDNA Synthesis, the Stranded Parameter in htseq-count, and Analysis of RNA-Seq Data. Preprints 2019, 2019030124 (doi: 10.20944/preprints201903.0124.v1). Srinivasan, K.; Virdee, S.; McArthur, A. Strandedness During cDNA Synthesis, the Stranded Parameter in htseq-count, and Analysis of RNA-Seq Data. Preprints 2019, 2019030124 (doi: 10.20944/preprints201903.0124.v1).

Abstract

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 (cDNA) 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.

Subject Areas

RNA-Seq, htseq-count, HISAT2, bioinformatics, strandedness

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