HAPPY

Hi-C data Analysis and Processing PIpeline (HAPPY). This software outputs the contact matrix with different bin sizes (resolutions): 1k, 5k, 10k, 50k, 100k.

Requirement

1. conda
2. snakemake
3. BWA-MEM
4. pairtools
5. cooler
6. SAMtools

conda and snakemake need to be installed manually and the rest will be automatically installed during the first launch of the program.

The output pair file can be easily filered based on provided condition.

Installation

git clone git@github.com:dawnmy/HAPPY.git

Usage

1. Adapt the config file for the pipeline Modify the config/config.yaml file in the program folder to adapt to your data location.

2. Download the reference genome and create BWA index and fasta index (.fai). For instance GRCh38 for homo sapiens:

wget https://www.encodeproject.org/files/GRCh38_no_alt_analysis_set_GCA_000001405.15/@@download/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta.gz -O GRCh38.fasta.gz

pigz -d GRCh38.fasta.gz
bwa index GRCh38.fasta
samtools fai GRCh38.fasta

3. Make the chromosome sizes file based on the .fai

cut -f1,2 GRCh38.fasta.fai > chrom.all.sizes

4. Launch the pipeline With 20 threads

snakemake -s runHiC.smk --use-conda -j 20

If you use SGE submission system:

snakemake -s runHiC.smk --use-conda -c "qsub -cwd -pe multislot {threads} -i /dev/null -v PATH" -j 2