RNA dot blot identified a potential locus of a methylated cytosine in 28S which increases its methylation in disease conditionsa and decreases under disease suppressor. A bisulfite sequencing was carried out to confirm the potential site, 3402 in 28S sequence pdb|3J3E|5. This repository contains the code used to analyse sequencing data.
Create and activate a conda environment
cd pilot
conda create --name methyl28s
conda activate methyl28s
conda install -c bioconda snakemake fastqc multiqc samtools deeptools bowtie2 trim-galore fastq-screen drmaa bismark
Download FASTQ files from the archive.
Run snakemake with the provided script. Please note this script might need to be modified to meet the needs of your computing cluster.
./run_snake.sh
This will trim adapters, perform quality control, download genome files and map reads with Bowtie2, run Bismark and create bedgraph files.
Once snakemake is finished, we suggest using RStudio. If this is done on a different machinge (I run RStudio on a laptop), some data need to be copied over (see ./get_data.sh and ./scripts/rsync_include.txt). Once in RStudio, start in the top project directory. The first step is to create environment using renv:
install.packages("renv")
renv::restore()
This will install all necessary packages. Run the targets pipeline.
targets::tar_make()
This will carry out all the calculations, create objects for the report. The report (./doc/pilot_report.qmd) can be created using
quarto::quarto_render("./doc/pilot_report.qmd", output_format = "html")
from the RStudio console.