ZARP: Supplementary materials
Creators: name: Katsantoni, Maria
name: Bąk, Maciej
name: Ataman, Meriç
name: Pozzan, Noè
name: Schlusser, Niels
name: Moon, Youngbin
name: Mironov, Aleksei
name: Börsch, Anastasiya
name: Kanitz, Alexander
Publisher: name: Zenodo
Year: 2024
Subjects: transcriptomics
RNA-seq
snakemake
quantification
singularity
conda
multiqc
mapping
pre-processing

description: This record supplements the F1000Research article on the ZARP workflow and its ZARP-cli command-line interface.

The following data are included:



zarp_use_cases.zip: Includes instructions (zarp_use_cases.md) and input data required to reproduce the use cases described in the manuscript.

mouse_sarcopenia_example_outputs.zip: Contains the cross-sample outputs (gene/transcript expression tables, PCA, MultiQC report and Snakemake report) produced by a ZARP run for the described 20-sample mouse sarcopenia RNA-seq experiment (not including indexes), as well as the sample-specific outputs for the smallest of the 20 samples.

zarp_cli_example_outputs.zip: Contains a representative fraction of the outputs produced by the described ZARP-cli runs; in particular, it contains the artifacts generated by the SRA download workflow for a single C. elegans sample (SRR21711080), the outputs produced by the HTSinfer workflow for all 25 samples (20 from the mouse sarcopenia dataset and 5 from the metadata inference demonstration run), the genome resources created by genomepy for the C. elegans genome WBcel235, and the C. elegans-specific ZARP workflow results, including indexes.


We would further like readers to note the following:



With respect to the latter two archives, data were selected in an effort to keep the record at an acceptable size, while still providing a representative and largely complete overview of ZARP and ZARP-cli outputs for reference and validation.

In all cases where files contained absolute file paths, we have manually replaced the real path prefixes with a dummy value (PATH/TO/MY/ANALYSIS), in order not to expose potentially sensitive details about the file system the analyses were run on.

We have deliberately not included ZARP, ZARP-cli and machine logs, as we feel that these may be too system-specific and potentially sensitive; we do, however, retain all logs in our archive, and will be willing to share them in response to reasonable requests.
description: Licensing information


Note that all script files in zarp_use_cases.zip (i.e., those with file extension .sh) are licensed under Apache 2.0, whereas all other files in that archive (file extensions .yaml and .tsv) are licensed under CC BY 4.0.

The mouse_sarcopenia_example_outputs.zip and zarp_cli_example_outputs.zip archives contain sample data from SRX7031689 and SRX17708425, respectively, and files derived from these and other data sets (including other RNA-seq libraries from the Sequencing Read Archive and genome resources provided by Ensembl) through the application of the ZARP pipeline and software tools contained therein. Unfortunately, we do not know exactly what this means with respect to how these data can be (re)used, so we would kindly ask you to only use them for your own personal needs, e.g., to validate the results you have obtained by reproducing the use cases described in zarp_use_cases.zip.
description: MK and MBak  were supported by the "Biozentrum PhD Fellowships" program.