bio-epitranscriptomics-merip-preprocessing

<!--
# COPYRIGHT NOTICE
# This file is part of the "Universal Biomedical Skills" project.
# Copyright (c) 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu>
# All Rights Reserved.
#
# This code is proprietary and confidential.
# Unauthorized copying of this file, via any medium is strictly prohibited.
#
# Provenance: Authenticated by MD BABU MIA

-->

---
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
measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes.
allowed-tools:
  - read_file
  - run_shell_command
---

# MeRIP-seq Preprocessing

## Alignment with STAR

```bash
# 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

```bash
# 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

```python
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


<!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE -->