Article
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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
Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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