docs/DEMO.md

In lehner-lab/DiMSum: A pipeline for processing deep mutational scanning data

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Demo

DiMSum STEAM Demo

In order to run the DiMSum STEAM demo (variant counts to fitness and error), no optional software is required (see Installation Instructions for details).

Simply type the following on the command-line:

DiMSum --runDemo T

A table of variant counts included in the DiMSum R package is processed and results are saved to a folder named 'DiMSum_Project' in the current working directory. Expected run time <10min.

Full DiMSum Demo (WRAP+STEAM)

REQUIRED: In order to run the full DiMSum demo (FASTQ files to variant fitness and error), FastQC, Cutadapt, VSEARCH and Starcode need to be installed (see Installation Instructions for details). If DiMSum was installed using the DiMSum bioconda package, these dependencies are installed by default. The full demo also requires demo FASTQ files, which can be downloaded from here.

Then, unzip the FASTQ folder and run the full demo from the command-line as follows:

unzip FASTQ.zip
DiMSum --runDemo T -i FASTQ

Results are saved to a folder named 'DiMSum_Project' in the current working directory. Expected run time <10min.

lehner-lab/DiMSum documentation built on April 10, 2024, 4:15 a.m.