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Welcome to the TranD project!

A preprint of the TranD manuscript is available here.

Pre-print Citation:

Nanni, A., Titus-McQuillan, J., Moskalenko, O., Pardo-Palacios, F., Liu, Z., 
     Conesa, A., Rogers, R. L., & McIntyre, L. M. (2021). The evolution of splicing: 
     transcriptome complexity and transcript distances implemented in TranD. 
     https://doi.org/10.1101/2021.09.28.462251 

TranD Table of Contents

Introduction to TranD:

User Guide

• For instructions on how to install and use TranD, with examples.

Output File Column Descriptions

• For a description of the various output files created by TranD and certain key utilities.

TranD Precomputed Data

• Contains TranD precomputed output files for 1GTF and 2GTF usage of TranD, as well as example Transcript Model Maps.

Transcript Model Map

• For a detailed guide following the data analysis pipeline used for creating a Transcript Model Map.

Utility Descriptions

• For a detailed explanation of each TranD utility: tools used in conjunction with TranD and tools that can further analyze TranD output.

Suggested Best Practices for Long Reads

• For an in-progress description of the best way to process long read data into an annotation that can be analyzed by TranD.

TranD Analysis Examples:

Drosophila Species Comparison

• Comparing Drosophila melanogaster and Drosophila simulans to show an example of using TranD to perform cross-species genome and transcriptome comparison

Long Read Method Comparison

• An example of comparing two long read methods using TranD and Drosophila data.

Human Annotation Comparison

• An example of comparing two annotation creation methods using TranD and human data.

New Data Requests

We take requests to produce additional precomputed data using our computational resources. Use TranD GitHub Issues to submit requests for new datasets.

Preprint

A preprint of the TranD manuscript is available here