Guttman Lab GitHub

RAP Probe Designer

A tool for designing capture or control probes for use in the RAP assay. This tool will allow you to design probes for a single RNA or batch across many RNAs as well as layout the probes on a custom microarray and optimize primer sequences at the ends of each probeset for selective amplification from complex synthesis pools.

Included in the RAP Probe Designer package:

  • RAP Probe Designer program
  • Program quick guide
  • Compatable primer3 executable

Ribosome Release Score (RRS)

A method for detecting translated regions using ribosome profiling data. The RRS measures ribosome release at bona fide stop codons to detect translation through ORFs. The program can score individual ORFs or identify the maximum RRS for any ORF within a transcript. This method robustly distinguishes between protein-coding genes and non-coding RNAs.

Included in the RRS package:

  • RRS program
  • ORF finder utility

SPRITE Pipeline

This repository contains all code for the Guttman Lab SPRITE pipeline.

  1. The main steps of this pipeline are:
    Identify barcodes in your sequenced reads.
  2. Align these reads to your genome of interest.
  3. Discard alignments that don’t meet certain criteria.
  4. Group alignments into clusters.
  5. Create heatmaps from clusters.

All of these steps have been automated using the Snakemake workflow management system.


Scripture is a method for transcriptome reconstruction that relies solely on RNA-Seq reads and an assembled genome to build a transcriptome ab initio. The statistical methods to estimate read coverage significance are also applicable to other sequencing data. Scripture also has modules for ChIP-Seq peak calling.

Learn more: read the publication


Scripture is actively maintained by the Garber Lab at UMass.