quartet_rna_project

This is an Image for RNA modification analysis of direct RNA-seq data, using dorado and modkit. It is built using Apptainer and can be run by both Apptainer and Singularity.

Getting Started

Installation

Below is an example of how you can set up the Image and run.

1. Download the sif file and load apptainer if have

   wget https://github.com/mritchielab/quartet_rna_project/blob/main/RNA_modification.def
   module load apptainer

2. Build Image (def file)

   apptainer build --fakeroot RNA_modification.sif RNA_modification.def

3. Read-to-run your sample now

   apptainer run --nv \
    --bind /Singularity/testdata:/input \
    --bind /Singularity/testresult:/output \
    --bind /project/reference:/reference \
    ./RNA_modification.sif \
    --input /input \
    --output /output \
    --ref /reference/gencode.v43.transcripts.fa \
    --model-dir /opt/dorado/models

Checking results

The pipeline produces BAM file from dorado basecaller, and bed file from modkit.