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reconstruction_celllines_patients.md

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Reconstruct ecDNA elements in cell lines and patient samples using Decoil.

4.1 Preprocess nanopore sequencing data from cell lines and patient samples

4.1.1 Run basecalling

Install using Nanopore Guideline, guppy_6.3.4. Per sample perform basecalling to transform fast5 to fastq.

sbatch ../ecDNA_reconstruction/run_basecalling.sh

4.1.2 Run preprocessing

This step is perform per sample and executes:

  • read filtering
  • QC
  • mapping
  • sv calling
  • coverage profile
# download snakmemake workflow
git clone git@github.com:henssen-lab/nano-wgs.git
cd nano-wgs

# uses an input file s.txt
# Run	          Sample   Patient	    Kit	        Flowcell
# <path_to_fastq> <p1_s1>  <p1>     SQK-LSK110	FLO-MIN106
# <path_to_fastq> <p1_s2>  <p1>     SQK-LSK110	FLO-MIN106
# <path_to_fastq> <p2_s1>  <p2>     SQK-LSK110	FLO-MIN106
# <path_to_fastq> <p2_s2>  <p2>     SQK-LSK110	FLO-MIN106
sbatch ../ecDNA_reconstruction/run_preprocessing.sh

4.2 Reconstruct ecDNA elements for cell lines and patient sample using Decoil

4.2.1 Install Decoil from source (version 1.1.2):

git clone https://github.com/madagiurgiu25/decoil-pre.git
cd  decoil-pre

# checkout release 1.1.2-slim
git checkout tags/1.1.2-slim

# create conda environment
mamba env create -f environment.yml
conda activate envdecoil

python -m pip install -r requirements.txt
python setup.py build install

# add decoil in $PATH
ROOT=`dirname $(which decoil)`
export PATH=$PATH:$ROOT

This is available also as docker container madagiurgiu25/decoil:1.1.2-slim.

4.2.2 Run reconstruction for cell lines

sbatch ../ecDNA_reconstruction/run_decoil_v112_07022024_slurmarray_celllines_hg19.sh
sbatch ../ecDNA_reconstruction/run_decoil_v112_07022024_slurmarray_celllines_hg38.sh

4.2.3 Run reconstruction for patient samples

sbatch ../ecDNA_reconstruction/run_decoil_v112_07022024_slurmarray.sh