Scripts to process and analyse GLORI and RNA-seq data for the manuscript: "Inhibition of METTL3 by STC-15 induces RNA misprocessing that results in dsRNA formation and activates innate immunity"
- GLORI processing steps:
- generate STAR index from A-to-G-converted, combined positive and reverse-complemented genome strands
- fastq A to G conversion
- fastq alignment to A to G converted genome (STAR)
- back conversion of aligned reads G to A
- count As and Gs at each A position in transcriptome (parallelized bcftools mpileup)
- calculate m6A proportions A/A+G
- filter for positions with A+G count ≥ 20 and m6A proportion ≥ 0.25
Raw data: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE312944