Surojit Biswas, Konstantin Kerner, Paulo Jose Pereira Lima Teixeira, Jeffery L. Dangl, Vladimir Jojic, Philip A. Wigge. "Tradict enables high fidelity reconstruction of the euykaryotic transcriptome from 100 marker genes." Submitted (2016). BioRxiv: http://biorxiv.org/content/early/2016/06/21/060111.
With the exception of data, this repository contains everything required to perform downloads from the SRA and recapitulate analyses performed in our paper. The repository is composed of several directories. Each is listed below with a description of its purpose and contents.
The release version of Tradict, as well as documentation and usage examples, are provided at https://github.com/surgebiswas/tradict. Separation of the tradict repository from this transcriptome_compression repository was done so that the release code was separate from all of the analysis scripts, which for the most part, won't be of practical interest to most users. Note that this transcriptome_compression repository contains the version of Tradict used to perform all analyses for the submitted version of the manuscript (current as of June 22, 2016). The main training and prediction scripts in this repository are named tradict_train_pmvn and tradict_predict_pmvn, respectively. However, in the tradict repository, these were renamed to tradict_train and tradict_predict, respectively.
The version of Tradict used in this repository will no longer be supported; users should find the latest version of Tradict at https://github.com/surgebiswas/tradict.
- data_download - Contains the custom scripts necessary to download and quantify raw RNA-Seq reads from NCBI's Short Read Archive (SRA). This repository contains it's own README that describes how to perform the data downloads. An overview of the download workflow is also given in the Materials and Methods section in the Supplemental Information of our paper.
- util - Contains accessory code used by analysis scripts. Code in this directory is commented as needed to explain function and usage.
- analysis -- Contains all code used to perform analysis and generate figures. The main analysis 'master scripts' are in the
AthalianaandMmusculussubfolders and have file names of the following form:analyze_X_transcriptome_compression.m. These master scripts contain blocks of code, demarcated byif-elseblocks, that each perform an analysis of the data or produce sub-panels of a figure. These scripts are commented to provide descriptions of what they are doing, as are all dependency scripts.
Send questions/comments to surojitbiswas@g.harvard.edu.