From 4e534f407ba2e2fc66782d77b97d116fe0b10093 Mon Sep 17 00:00:00 2001 From: Mariya Lysenkova Date: Tue, 7 Mar 2023 09:21:47 +0100 Subject: [PATCH] Update README --- README.md | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index ac025e3..8588416 100644 --- a/README.md +++ b/README.md @@ -1,20 +1,22 @@ # REH cell line digital karyotyping ## Citation -This is a public repository containing scripts described in the publication "A complete digital karyotype of the B-cell leukemia REH cell line resolved by long-read sequencing" (Manuscript) +This is a public repository containing scripts described in the publication: + +Lysenkova Wiklander et al. +"A complete digital karyotype of the B-cell leukemia REH cell line resolved by long-read sequencing" ## Data -Primary data for this project are available at NCBI/SRA under the BioProject accession numbers PRJNA600820 and PRJNA834955. These data have been analyzed on a HPC using the commands in `01_hpc_processing`. The resulting analysis datasets are available at https://doi.org/10.5281/zenodo.7702098. +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.7702098. ## 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. - -### R and Python scripts +For HPC scripts, the full paths to source files have been omitted for simplicity. You will need to adjust them to your environment. -To run the R and Python scripts in this repository, you will need to do the following: +### 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