Reproducing Preferential Allele Expression Analysis Identifies Shared Germline and Somatic Driver Genes in Advanced Ovarian Cancer Halabi, Najeeb M., et al. "Preferential allele expression analysis identifies shared germline and somatic driver genes in advanced ovarian cancer." PLoS genetics 12.1 (2016): e1005755.
- Reproducibility is
- Main objective: reproduce all plots and charts in the paper.
- Can the process be run in a reasonable amount of time on AWS?
- Does using the latest versions of the software packages used in the original paper result in different outcomes?
The study used both exome and RNA sequence data. A table containing metadata on each sample can be found here
The authors provided their RNA and exome sequence data (28 samples in total) on the GEO
database with accession number GSE75935. Querying GEO with this accession number, we found and
downloaded the sequences associated with the study - all 28 sequences associated with the
Sequence Read Archive (SRA) identifier SRP067276. To download the data, we used the prefetch
command in the National Center for Biotechnology Information's SRA toolkit (installation instructions available
here). To
convert the SRA files to fastq format, we used the fastq-dump command. Shell scripts to
download and convert the files can be found in the [scripts folder][./scripts] of this
repository].
- Docker