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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

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