**    **     **        *******
//**  **     ****      /**////**
 //****     **//**     /**   /**
  //**     **  //**    /*******
   /**    **********   /**////
   /**   /**//////**   /**
   /**   /**     /**   /**
   //    //      //    //

Install

To install this latest version:

pip install git+https://github.com/wangwl/cemba_data

Documentation

1. Make sure create the right environment

git clone https://github.com/wangwl/cemba_data.git
mamba env create -f cemba_data/env.yaml
conda activate yap

Or directly read from http:

mamba env create -f https://raw.githubusercontent.com/DingWB/cemba_data/master/env.yaml
conda activate yap

2. Generate config.ini

yap default-mapping-config --mode m3c --barcode_version V2 --bismark_ref "~/Ref/hg38/hg38_ucsc_with_chrL.bismark1" \
      --genome "~/Ref/hg38/hg38_ucsc_with_chrL.fa" --chrom_size_path "~/Ref/hg38/hg38_ucsc.main.chrom.sizes"  \
      > config.ini
# pay attention to the path of reference, should be the same as on the GCP if you are going to run the pipeline on GCP.      

3. Demultiplex

yap demultiplex --fastq_pattern "test_fastq/*.gz" -o mapping -j 4 --aligner bismark --config_path config.ini

4. Run mapping

Run on local computer or HPC

sh mapping/snakemake/qsub/snakemake_cmd.txt

Run on GCP manually

scp mapping/AMB_220510_8wk_12D_13B_2_P3-5-A11/Snakefile highmem1:~/sky_workdir
scp -r mapping/AMB_220510_8wk_12D_13B_2_P3-5-A11/fastq highmem1:~/sky_workdir
# GCP
mamba env create -f https://raw.githubusercontent.com/DingWB/cemba_data/master/env.yaml
mkdir -p ~/Ref && gsutil -m cp -r -n gs://wubin_ref/hg38 ~/Ref
prefix="mapping_example/mapping/test/AMB_220510_8wk_12D_13B_2_P3-6-A11"
snakemake --snakefile ~/sky_workdir/Snakefile -j 8 --default-resources mem_mb=100 --resources mem_mb=50000 --config gcp=True --default-remote-prefix ${prefix} --default-remote-provider GS --google-lifesciences-region us-west1 --keep-remote -np

Run on GCP automatically

yap update-snakemake -o mapping -t m3c_skypilot_template.yaml

# spot
sky spot launch -y mapping/snakemake/gcp/AMB_220510_8wk_12D_13B_2_P3-3-A11.yaml

YAP (Yet Another Pipeline)

Pipeline(s) for mapping and cluster-level aggregation of single nucleus methylome and multi-omic datasets. Technologies supported:

• snmC-seq(1/2/3)
• snmCT-seq (mC + RNA)
• snmC2T-seq (mC + RNA + Chromatin Accessibility)
• snm3C-seq (mC + Chromatin Conformation)
• any NOMe treated version of the above

See Documentation