This repository contains the R code used in the analysis of RRBS data in the manuscript entitled "Juvenile exposure to imazalil disrupts epigenetic and transcriptomic regulation of hepatic energy metabolism in Xenopus tropicalis".
Raw RRBS and RNAseq fastq files have been deposited in the European Nucleotide Archive (ENA) at EMBL-EBI under accession PRJEB86528.
RRBS data were processed using the Nextflow nf-core/methylseq pipeline version 2.6.0 using the following commmand.
nextflow run nf-core/methylseq -r 2.6.0 \
-profile uppmax \
--input "samplesheet_IMZ_05-24.csv" \
--aligner 'bismark' \
--pbat \
--clip_r1 2 \
--three_prime_clip_r2 2 \
--skip_deduplication \
--fasta "/crex/proj/snic2020-5-486/mauricio/ensembl_Xtro_genome/Xenopus_tropicalis.UCB_Xtro_10.0.dna_sm.toplevel.fa"The Bismark .cov files were used as input. The analysis was divided in different R scripts for each step, located in RRBS/code. The complete pipeline was run through a quarto report file, rendered in RRBS/code/render_quarto_reports.R with specific parameters for each group.
RNAseq data were processed with nf-core/rnaseq version 3.12.0
nextflow run nf-core/rnaseq -r 3.12.0 \
-profile uppmax
--fasta Xenopus_tropicalis.UCB_Xtro_10.0.dna_sm.toplevel.fa \
--gtf Xenopus_tropicalis.UCB_Xtro_10.0.110.gtf \
--input file_list.csv \
--extra_trimgalore_args '--clip_R1 1 --clip_R2 1' \Salmon transcript quantification files were used as input and summarized at the gene level. RNAseq analysis code is located in RNAseq/code, and run as a quarto report in quarto/quarto_report.qmd