Code for working with nanopore sequencing data collected in altered gravitointertial environments, such as during parabolic flight. For details on processing acceleration data from parabolic flights, see the related repository: https://github.com/CarrCE/zerog
Tested with MATLAB 2019b on OS X 10.13. Expected to work with MATLAB 2019a. Requires the Statistics and Bioinformatics toolboxes. Because one of the datafiles is large, 32 GB memory is recommended.
Carr CE, Bryan NC, Saboda K, Bhattaru SA, Ruvkun G, Zuber MT. Nanopore Sequencing at Mars, Europa, and Microgravity Conditions. In preparation.
See also: Carr CE, Bryan NC, Saboda KN, Bhattaru SA, Ruvkun G, Zuber MT. Acceleration Profiles and Processing Methods for Parabolic Flight. npj Microgravity 4, Article number: 14 (2018) https://doi.org/10.1038/s41526-018-0050-3. Preprint: arXiv:1712.05737 https://arxiv.org/abs/1712.05737
Download: https://github.com/CarrCE/zerogseq/archive/master.zip or use command line git clone git@github.com:CarrCE/zerogseq.git.
Unzip to preferred location, here denoted /zerogseq-master.
Data is downloaded automatically by a MATLAB script. This is the recommended approach to ensure data is in the expected locations.
Direct access to sequencing and vibration data: https://osf.io/n6krq/ There are many files required, and after downloading the multipart zip files of sequencing data must be merged and unzipped. Thus, it is recommended to use the MATLAB script to automatically download, merge, and unzip the multipart zip archives. Instructions are included at the link.
Direct access to accelerometer data: Download: https://osf.io/5rqu9/download. This 1.0 GB (compressed ZIP) dataset has a CC BY 4.0 US license. More details at: https://osf.io/nk2w4/
Direct access to accelerometer analysis results: The analysis results are also available (188 MB ZIP) at: https://osf.io/pmhj4/download
In MATLAB, go to your /zerogseq-master path, and run the main script: zerogseq. This will perform the same analysis as in the publication (see citation, above), running each script in turn, including running some twice, once each on the "Flight" or "Ground" datasets. See each script for details and instructions.
The analysis may take up to 5-6 hours.
The results of running this analysis in MATLAB include a series of EPS and/or PDF figures, replicating those in the paper, and various tab-delimited files. All times are elapsed time, and for reference, the start time is: 2017-11-17 18:28:51 UTC.
Distributed under an MIT license. See LICENSE for details.