diff --git a/README.md b/README.md index 8588416..9d18925 100644 --- a/README.md +++ b/README.md @@ -4,13 +4,13 @@ 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" +"A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing" ## 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.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.108757278. ## Instructions -The scripts are numbered in the order they should be executed. +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. @@ -21,7 +21,7 @@ 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 +- 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` @@ -38,9 +38,9 @@ data/sv_callsets: - pb.sniffles.vcf data/fusion_callsets/long_read: -- cupcake.long.csv -- cupcake.std.csv -- jaffa_results.csv +- cupcake.long.csv +- cupcake.std.csv +- jaffa_results.csv data/fusion_callsets/short_read: - GM12878.fusionreport.txt @@ -50,4 +50,4 @@ data/fusion_callsets/short_read: - REH.fusioncatcher.fusion-genes.txt - REH.pizzly.txt - REH.squid.fusions.annotated.txt -- REH.starfusion.abridged.tsv \ No newline at end of file +- REH.starfusion.abridged.tsv