Linkage Analysis
Linkage analysis for variants in linkage with lead variants used LD Proxy and LD Matrix
Micro RNA binding
3' UTR effects of rs35624553 were determined using TargetScan, miRdSNP, and MicroSNiPer
Splicing
SpliceAI masked splicing predictions were downloaded from the github repository.
Splicing quantitative trait loci (sQTLs) were identified in the GTEx Database
Chromatin accessibility and transcription factor binding prediction
deepHaem was implemented using run_deephaem_4k_predictions.sh
Sasquatch was run using default Workflow 3 settings (7-mer, propensity-based [Erythroid], exhaustive) on the web interface. The rs17713054 allele specific accessibility profiles were generated with sasquatch_plot_RPTC_rs17713054.R.
Analysis scripts for element accessibility are in enhancer_accessibility
Allelic bias analysis
Analysis with WASP used an adapted Snakemake pipeline. More information can be found in the CRAN package documentation. Adapted scripts are in: wasp_pipe_for_covid_gwas
3C analysis
Domain inferral for probe design used the 3D genome browser and probes were designed using Capsequm2.
NuTi/NG Capture-C replicate data were first processed with CCSeqBasicS before being combined with CaptureCompare. Run scripts and custom CaptureCompare scripts are in capture_c_scripts
MCC analysis codes are available for academic use with input files in mcc_scripts.
LanceOtron interaction calling commands can be found in LanceOtron_MCC.py
Expression analysis
GTEx Calculator was used to determine eQTL genes for rs17713054.
Colocalisation analysis
Colocalisation of eQTL and GWAS signals used Coloc. The runshell used is coloc_analysis.R
Editing ICE analysis
Editing efficiency calculation used the Synthego ICE webtool.
ChIP/ATAC-seq mapping
Reads were mapped using NGseqBasic.
Spatial Transcriptomics
Modules and cell types were identified using WGCNA and Deconvolution. For further information see Cross et al. Further analysis was implemented in R with: Spatial_analysis.R