Multi-perspective quality control of Illumina RNA sequencing data analysis.
Quality control (QC) is a critical step in RNA sequencing (RNA-seq). Yet, it is often ignored or conducted on a limited basis. Here, we present a multi-perspective strategy for QC of RNA-seq experiments. The QC of RNA-seq can be divided into four related stages: (1) RNA quality, (2) raw read data (FASTQ), (3) alignment and (4) gene expression. We illustrate the importance of conducting QC at each stage of an RNA-seq experiment and demonstrate our recommended RNA-seq QC strategy. Furthermore, we discuss the major and often neglected quality issues associated with the three major types of RNA-seq: mRNA, total RNA and small RNA. This RNA-seq QC overview provides comprehensive guidance for researchers who conduct RNA-seq experiments.
Quanhu
Q
Sheng
Kasey
K
Vickers
Shilin
S
Zhao
Jing
J
Wang
David C
DC
Samuels
Olivia
O
Koues
Yu
Y
Shyr
Yan
Y
Guo
D000818:Animals; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D051379:Mice; D035683:MicroRNAs / Q000235:genetics; D011786:Quality Control; D017423:Sequence Analysis, RNA / Q000379:methods*; D013223:Statistics as Topic
D035683:MicroRNAs
RNA-seq; alignment; gene expression; quality control; raw data; small RNA-seq; total RNA-seq
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