REH cell line multi-omics

Citation

This is a public repository containing scripts described in the publication:

Lysenkova Wiklander et al. "A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing" https://doi.org/10.26508/lsa.202302481

Data

Sequencing data and BAM files for this project are available at NCBI/SRA under the BioProject accession numbers PRJNA600820 and PRJNA834955. These data have been analyzed on a high performance cluster (HPC) using the commands in 01_hpc_processing. The resulting analysis datasets are available at https://doi.org/10.5281/zenodo.108757278.

Instructions

The scripts are numbered in the order they should be executed.

HPC Bash Scripts

For HPC scripts, the full paths to source files have been omitted for simplicity. You will need to adjust them to your environment.

Other scripts

To run the other scripts in this repository, you will need to do the following.

Install:

R 4.2.1 and an integrated environment, e.g. RStudio
R packages: chromoMap, RColorBrewer, VennDiagram
Python 3.8
Necessary Python packages: pip install -r requirements.txt
SURVIVOR v1.0.7 built from: https://github.com/fritzsedlazeck/SURVIVOR and placed in the directory 02_sv_callset_analysis/bin

Download the files from Zenodo and place them in the following directories:

data/coverage:

copycat.ont.coverage.10kb.csv
copycat.pb.coverage.10kb.csv
copycat.pcrfree.coverage.10kb.csv

data/sv_callsets:

illumina.tiddit.vcf
ont.sniffles.vcf
pb.sniffles.vcf

data/fusion_callsets/long_read:

cupcake.long.csv
cupcake.std.csv
jaffa_results.csv

data/fusion_callsets/short_read: