DNA Methylation Analysis Using Bismark-Bowtie2

Bisulfite analysis was performed using Bismark-bowtie 2 (https://www.bioinformatics.babraham.ac.uk/projects/bismark/). We used the default Bowtie2 implementation of Bismark with the specifications that only uniquely mapped reads should be aligned. All alignments were performed with high stringency allowing for only one base mismatch (n = 1). We also clearly specified that no discordant pairs of the pair-end reads should be aligned. DNA methylation in the CG, CHG, and CHH contexts was calculated by dividing the total number of aligned methylated reads by the total number of methylated plus un-methylated reads.

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Hoguin A., Yang F., Groisillier A., Bowler C., Genovesio A., Ait-Mohamed O., Vieira F.R, & Tirichine L. (2023). The model diatom Phaeodactylum tricornutum provides insights into the diversity and function of microeukaryotic DNA methyltransferases. Communications Biology, 6, 253.

Publication 2023

Bisulfite Dna methylation

Corresponding Organization :

Other organizations : Inserm, Institut de Biologie de l'École Normale Supérieure, Université Paris Sciences et Lettres, Centre National de la Recherche Scientifique, Nantes Université, Unité en Sciences Biologiques et Biotechnologies de Nantes

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Variable analysis

independent variables

Bisulfite analysis method (Bismark-bowtie 2)

dependent variables

DNA methylation levels in CG, CHG, and CHH contexts

control variables

Bowtie2 implementation with only uniquely mapped reads aligned
High stringency alignment with one base mismatch allowed (n = 1)
No discordant pairs of pair-end reads aligned

controls

No positive or negative controls were explicitly mentioned in the provided information.

Annotations

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