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Sequencing Data Analysis

SL Si-Yu Liu
JW Jun-Jie Wu
ZC Zhong-hua Chen
MZ Ming-Li Zou
YT Ying-ying Teng
KZ Kai-Wen Zhang
YL Yue-Yue Li
DG Dang-yang Guo
FY Feng-Lai Yuan
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Briefly, paired-end reads were harvested from an Illumina HiSeq 4000 sequencer and were quality controlled by Q30. After 3′ adaptor-trimming, low quality reads were removed by cutadapt software (v1.9.3). First, clean reads of all libraries were aligned to the reference genome (HG19) by Hisat2 software (v2.0.4). Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps. These peaks identified by both software overlapping with exons of mRNA were figured out and chosen by home-made scripts. Identified m6A peaks were subjected to motif enrichment analysis by HOMER (Heinz et al., 2010), while the compared reads can be visualized in the Integrative Genomics Viewer (IGV) to visually show the expression of mRNA (Thorvaldsdóttir et al., 2013). GO and pathway enrichment analysis were performed by the differentially methylated protein coding genes.

Copyright and License information:  ©2021 Liu, Wu, Chen, Zou, Teng, Zhang, Li, Guo and Yuan.
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