COSMOS 2023 - Long-read analysis of C2C12 Differentiation.

Instructions

1. Clone this repository in your folder on the UCI HPC git clone https://github.com/jazsakr/cosmos2023_c2c12_smk.git
2. Run the set-up script and follow the on-screen instructions bash set-up.sh
3. Run the script that runs snakemake file bash run_smk.sh

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Description

Samples

C2C12 myoblasts were differentiated into myotubes and made into long-read Nanopore libraries.

Preprocessing

The following is provided for you:

• Basecalled and trimmed reads
• Mouse reference genome and annotation

Long-read Pipeline:

This workflow uses snakemake to run the long-read pipline using TranscriptClean and TALON.

Step 1: initial setup

Running the set-up.sh script does the following: - install package manager conda and mamba - configure conda by adding channels - clone long-read packages TranscriptClean and TALON - create environment with snakemake and TALON installed

Step 2: run snakemake

Runing the run_smk.sh script does the following: - Map to genome using minimap2 - Reverse flipped reads with custom script - Reference-based error correction using TranscriptClean - Quantify and categorize transcripts using TALON

Snakemake workflow: