bio-epitranscriptomics-merip-preprocessing

npx skills add BioTender-max/awesome-bio-agent-skills --skill merip-preprocessing --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

## 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. ```bash # Build index (once) STAR --runMode genomeGenerate \ --genomeDir star_index \ --genomeFastaFiles genome.fa \ --sjdbGTF

Build index (once)
STAR --runMode genomeGenerate \
Align IP and input samples
for sample in IP_rep1 IP_rep2 Input_rep1 Input_rep2; do
STAR --genomeDir star_index \
done
Index BAMs
for bam in *Aligned.sortedByCoord.out.bam; do
samtools index $bam
Check IP enrichment