bio-epitranscriptomics-merip-preprocessing - SKILL.md Agent Skill

name: bio-epitranscriptomics-merip-preprocessing description: Align and QC MeRIP-seq IP and input samples for m6A analysis. Use when preparing MeRIP-seq data for peak calling or differential methylation analysis. tool_type: cli primary_tool: STAR

Version Compatibility

Reference examples tested with: STAR 2.7.11+, deepTools 3.5+, samtools 1.19+

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

Python: pip show <package> then help(module.function) to check signatures
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 Preprocessing

"Preprocess my MeRIP-seq IP and input samples" → Align and QC methylated RNA immunoprecipitation sequencing data, comparing IP enrichment to input for downstream m6A peak calling.

CLI: STAR for splice-aware alignment, samtools for post-processing, deepTools for QC

Alignment with STAR

Goal: Align MeRIP-seq IP and input samples to the genome with splice-aware mapping for downstream peak calling.

Approach: Build a STAR genome index with gene annotations, then loop through all IP and input samples to produce coordinate-sorted BAM files.

# Build index (once)
STAR --runMode genomeGenerate \
    --genomeDir star_index \
    --genomeFastaFiles genome.fa \
    --sjdbGTFfile genes.gtf

# Align IP and input samples
for sample in IP_rep1 IP_rep2 Input_rep1 Input_rep2; do
    STAR --genomeDir star_index \
        --readFilesIn ${sample}_R1.fastq.gz ${sample}_R2.fastq.gz \
        --readFilesCommand zcat \
        --outSAMtype BAM SortedByCoordinate \
        --outFileNamePrefix ${sample}_
done

QC Metrics

# Index BAMs
for bam in *Aligned.sortedByCoord.out.bam; do
    samtools index $bam
done

# Check IP enrichment
# Good MeRIP: IP should have peaks, input should be uniform
samtools flagstat IP_rep1_Aligned.sortedByCoord.out.bam

IP/Input Correlation

import deeptools.plotCorrelation as pc

# Check replicate correlation
multiBamSummary bins \
    -b IP_rep1.bam IP_rep2.bam Input_rep1.bam Input_rep2.bam \
    -o results.npz

plotCorrelation -in results.npz \
    --corMethod spearman \
    -o correlation.png

Related Skills

read-qc/quality-reports - Raw read quality assessment
read-alignment/star-alignment - General alignment concepts
m6a-peak-calling - Next step after preprocessing