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.
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:
pip show <package> then help(module.function) to check signatures<tool> --version then <tool> --help to confirm flagsIf code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
"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.
STAR for splice-aware alignment, samtools for post-processing, deepTools for QCGoal: 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
# 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
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