m⁶A-CAMseq

Qucik start

step 1. Prepare configuration file

minimum configuration example:

workdir: workspace

# can be "ECLIP10", "ECLIP6", "TAKARAV3", "SACSEQV3", "STRANDED"
libtype: ECLIP10

# TODO: if the genome index is not available, the pipeline will build it automatically
genome_index: /data/reference/genome/Arabidopsis_thaliana/hisat2_tx_3n/TAIR10.release57

reference:
  contamination:
    # Multiple contaminant reference files are allowed
    - ref/Agrobacterium.fa.gz
  genes:
    # Multiple gene reference files are allowed
    - ref/spikein.fa
    - ref/ERCC92.fa
    - ref/cress_rRNA.fa
  genome:
    # Only one genome is allowed
    - /data/reference/genome/Arabidopsis_thaliana/TAIR10.fa

samples:
  cress1:
    data:
      - R1: data/cress1_R1.fq.gz
        R2: data/cress1_R2.fq.gz
  cress2:
    data:
      - R1: data/cress2_R1.fq.gz
        R2: data/cress2_R2.fq.gz

Warning

different from previous version (v1), a 3rd level of "data:" tag is added into "samples:" section this is a preserved behavior for future expansion

advanced configuration: please refer to docs/configuration.md

step 2: Install apptainer and run

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

Tip

apptainer cannot detect mounted partitions by default, you need to add -B /partition_name flag right after the run command.

Tip

If you work on a remote server with internet access, you can compile the pipeline first

apptainer build camseq.sif docker://y9ch/camseq:v2
apptainer run camseq.sif -c data.yaml -j 48

Tip

For using the previous version of pipeline (v1), try:

apptainer run docker://y9ch/camseq:v1 -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/

Changelog

• update in May 11, 2025

  • data processing steps is now based on trichromat
  • m6A site detection and filtering is now automatically and have been combined with the pipeline

• update in May 13, 2025 (v2.1)

  • the m6A calling step is also based on trichromat
  • the rate limiting step from the 3n-table has been removed

 

Copyright © 2023-present Chang Y