Browser and CLI
Run interactively from a standalone local HTML application or automate analyses with the Linux x86-64 CLI.
TranscriptPeak v1.11.2
Peak calling directly in transcript coordinates.
TranscriptPeak analyzes meRIP-seq / m6A-seq and RIP-seq BAM files aligned to transcript sequences. The current release adds transcript-to-gene mapping to the v1.11 peak-calling workflow and provides both browser and Linux command-line interfaces.
What it does
TranscriptPeak workflow.
Purpose-built scientific software with downloadable documentation and reproducible local workflows.
Assay-specific peak calling
Dedicated meRIP/m6A-seq and RIP-seq modes use different spatial defaults for windows, steps, merging and smoothing.
Hard fold filter
Version 1.11.2 enforces the minimum fold threshold as a final filter on every reported peak.
Transcript-to-gene mapping
Optional mapping files add gene IDs/names with tolerant transcript-ID normalization.
Coverage and motifs
The browser build provides IGV-style coverage inspection and sequence/motif summaries.
Reproducible outputs
TSV, BED, JSON, peak FASTA, transcript-region table, parameter JSON, summary and optional motif output.
Usage
CLI example.
For browser use, extract the HTML ZIP and open the enclosed HTML file. For batch processing, use the CLI:
transcriptpeak_v1.11.2 callpeak \ -assay rip \ -f transcripts.fa \ -t RIP_rep1.bam RIP_rep2.bam \ -c Input_rep1.bam Input_rep2.bam \ --gene-map transcript_to_gene.tsv \ -n HuR --outdir HuR_TranscriptPeak
Install / launch
Start the release locally.
tar -xzf TranscriptPeak_CLI_v1.11.2_linux_x86_64.tar.gz cd TranscriptPeak_CLI_v1.11.2_linux_x86_64 chmod +x transcriptpeak_v1.11.2 ./transcriptpeak_v1.11.2 --help
Research-use software. BAM transcript/reference names and the transcript FASTA must describe the same transcriptome build. Validate peak calls independently.