Convert Salmon output to Sleuth-compatible format

Program introduction

What is Sleuth?

Sleuth is a program that performs differential expression analysis of gene isoforms using the transcript abundance estimates output from alignment-free methods, such as Sailfish, Salmon and Kallisto.

What is wasabi?

Wasabi is a program that converts Sailfish and Salmon output for downstream analysis with Sleuth.

Format conversion

We use Wasabi to prepare Salmon output for downstream analysis with sleuth

$ cd /home/USER/SSAPs
$ R

Define the file path to Salmon (and STAR+Salmon) quant directories

  • The "Salmon" mapping strategy is described here

  • The "STAR + Salmon" strategy is described here

  • The "Salmon with bootstrap" strategy is described here

library(wasabi)

# Salmon
files1 = file.path("salmon", list.files("salmon"))

# STAR + Salmon
files2 = file.path("salmon_star", list.files("salmon_star"))

# Salmon with bootstrap
files3 = file.path("salmon-bs", list.files("salmon-bs"))

Run the prepare_fish_for_sleuth function to start conversion

The function will create abundance.h5 files in sleuth-compatible format in the same directory as the Salmon quant.sf files

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