Associated code for "The Landscape of N6-Methyladenosine in Localized Primary Prostate Cancer"

Notes shown below where applicable

Pipelines

A_ProcessingRawData

• Read alignment and quality control
• Generation of BigWig files

B_PeakCalling

• Calling peaks using MeTPeak and exomePeak
• Calling motifs using HOMER

C_SubsamplingPeakAnalysis

• Subsampling reads from the IP and Input library and evaluating their impact on peak calling
• Results used to generate Supplementary Figure 2C-D

D_RNAseqGermlineVariants

• Calling germline variants using the Input library and comparing them to the variants called in Houlahan et al., 2019
• Results used to generate Supplementary Figure 1E

E_HistogramZoo

• Calling joint peaks using HistogramZoo

F_DataNormalization

• Normalizing and adjusting IP data by Input data

G_AllelicImbalance

• Generating allelic-specific reads for Figure 3A

H_m6AQTLAnalysis

• Quality control of germline variants
• Testing Plink/PEER covariates
• Generating input files and running MatrixQTL

I_HypoxiaCellLines

• Processing hypoxia cell line meRIP-seq data

J_TumourNormal

• Processing tumour normal meRIP-seq data

SAC-seqProcessing

• Data processed following code from https://github.com/shunliubio/m6A-SAC-seq_new_protocol

Figures

Figure 3

• The code for Figure 3B is provided in the code for Supplementary Figure 4D-F
• The code for Figure 3C is provided in the code for Figure 1A
• The code for Figure 3E-F is provided in the code for SupplementaryFigure 4G

Figure 4

• Code provided for Figure 4A

Figure 5

• Code provided for Figure 5B, E, J, K

Supplementary Figures

Supplementary Figure 1

• Supplementary Figures 1A-B were drawn rather than coded
• Supplementary Figure 1E - Data generated from D_RNAseqGermlineVariants pipeline

Supplementary Figure 2

• Supplementary Figure 2C-D - Data generated from C_SubsamplingPeakAnalysis pipeline
• Supplementary Figures 2G-J are addressed by Figure1/B-E_GeneProfilePlots.R

Supplementary Figure 4

• Code provided for bigWig processing for producing Figure 4 D & E

Supplementary Figure 5

• Supplementary Figures 5A & 5B are from the ConsensusClusterPlus package

Supplementary Figure 6

• code for Supplementary Figure 6C is in Figure1/A_Overview.R (see idc_boxplot)
• code for Supplementary Figure 6D is in Figure1/A_Overview.R (see clinical_dotmap)

Supplementary Figure 7

• Supplementary Figures 7A & 7J were drawn rather than coded
• The code for Supplementary Figure 7I is provided in the code for Figure 1A