m⁶A-CAMseq

Qucik start

• Prepare configuration file

reference:
  genes:
    - ../test/spike-in.fa
    - ../test/ERCC92.fa
    - ~/reference/rRNA/Arabidopsis_thaliana.rRNA.fa
  genome:
    - /data/reference/genome/Arabidopsis_thaliana/TAIR10.fa

# TODO: automatically generate index (?)
genome_index: /data/reference/genome/Arabidopsis_thaliana/hisat2_tx_3n/TAIR10.release57

samples:
  test1:
    - R1: ../test/test_R1.fq.gz
      R2: ../test/test_R2.fq.gz

• Install apptainer and run

apptainer run -B /data docker://y9ch/camseq -c data.yaml -j 48

Customization

System Requirements

This package has been tested on Linux operating systems. It requires the following software dependencies:

• Python 3.7 or higher
• Snakemake 8.0.0 or higher
• hisat2-3n
• cutseq

Documentation

The documentation is available at https://y9c.github.io/m6A-CAMseq/

 

Copyright © 2023-present Chang Y