epitranscriptomics-m6a-peak-calling

epitranscriptomics-m6a-peak-calling is a Bioinformatics & life sciences skill for AI agents, published by swaruplab in the operon repository on GitHub. Skillspace rates epitranscriptomics-m6a-peak-calling C (76/100) and it passed the safety scan; the rating is based on static analysis only.

Calls m6A peaks from MeRIP-seq / m6A-seq paired IP-vs-input data using exomePeak2 (transcript-aware, GC-bias-corrected Poisson GLM; Liu 2022 *NAR Genom Bioinform* 4:lqac046), MeTPeak (HMM over sliding windows; Cui 2016 *Bioinformatics* 32:i378), MACS3 / MACS2 with --nomodel --broad --keep-dup all (genome-wide broad alternative), and DRACH motif enrichment confirmation via HOMER or ggseqlogo as a sanity check (NOT a filter). Covers BED12 vs narrowPeak output formats, exonic vs intronic peak handling, multi-tool reconciliation (intersection vs union; cross-caller IDR-equivalent), the m6A-vs-m6Am ambiguity at 5'UTR peaks that antibody-based methods cannot resolve, and orthogonal-validation routes (miCLIP / GLORI / m6A-SAC-seq / m6Anet). Use when calling peaks from paired IP/input genome BAMs, choosing exomePeak2 (transcript-aware default) vs MACS3 (broad genomic) vs MeTPeak (HMM-smoothed low-coverage), confirming DRACH enrichment as a sanity check on the peak set as a whole, reconciling…

Grade

C

Quality

76 / 100

Safety

Passed

GitHub stars

90

Unproven: rated by static analysis only, not yet compared head-to-head.

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