bio-workflows-merip-pipeline

Version Compatibility

Reference examples tested with: DESeq2 1.42+, MACS3 3.0+, STAR 2.7.11+, bedtools 2.31+, fastp 0.23+, samtools 1.19+

Before using code patterns, verify installed versions match. If versions differ:

• R: packageVersion('<pkg>') then ?function_name to verify parameters
• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

MeRIP-seq Pipeline

"Analyze my MeRIP-seq data from FASTQ to differential m6A peaks" → Orchestrate read alignment (STAR), m6A peak calling (exomePeak2/MACS3), differential modification testing, and metagene/Guitar visualization of modification sites.

Pipeline Overview

FASTQ → QC → Align IP+Input → Peak calling → Annotation → Differential → Visualization

Step 1: Quality Control

fastp -i IP_R1.fq.gz -I IP_R2.fq.gz \
    -o IP_R1_trimmed.fq.gz -O IP_R2_trimmed.fq.gz \
    --json IP_fastp.json --html IP_fastp.html

fastp -i Input_R1.fq.gz -I Input_R2.fq.gz \
    -o Input_R1_trimmed.fq.gz -O Input_R2_trimmed.fq.gz \
    --json Input_fastp.json --html Input_fastp.html

Step 2: Alignment

STAR --genomeDir star_index \
    --readFilesIn IP_R1_trimmed.fq.gz IP_R2_trimmed.fq.gz \
    --readFilesCommand zcat \
    --outSAMtype BAM SortedByCoordinate \
    --outFileNamePrefix IP_

STAR --genomeDir star_index \
    --readFilesIn Input_R1_trimmed.fq.gz Input_R2_trimmed.fq.gz \
    --readFilesCommand zcat \
    --outSAMtype BAM SortedByCoordinate \
    --outFileNamePrefix Input_

samtools index IP_Aligned.sortedByCoord.out.bam
samtools index Input_Aligned.sortedByCoord.out.bam

Step 3: Peak Calling with exomePeak2

library(exomePeak2)
library(TxDb.Hsapiens.UCSC.hg38.knownGene)

result <- exomePeak2(
    bam_ip = c('IP_rep1.bam', 'IP_rep2.bam'),
    bam_input = c('Input_rep1.bam', 'Input_rep2.bam'),
    txdb = TxDb.Hsapiens.UCSC.hg38.knownGene,
    genome = 'hg38'
)

peaks <- exomePeaks(result)
exportResults(result, format = 'BED', file = 'm6a_peaks.bed')