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CPTRA | A software package for cross-platform transcriptome analysis

Analyzes transcriptome sequencing data from different sequencing platforms including Solexa and SOLiD short. CPTRA is a software allowing the merging of various data to identify novel genes in species. The application first groups every sequence tags and gives a count number for each of these. Then, it aligns them to the cDNA sequences according specified rules for finally using the results to calculate normalized expression counts for each cDNA sequence.

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CPTRA forum

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CPTRA classification

CPTRA specifications

Unique identifier:
OMICS_01303
Software type:
Package/Module
Restrictions to use:
None
Output data:
Some tag alignment result files and GO categorization results.
Programming languages:
Python
Stability:
Stable
Name:
Cross Platform Transcriptome Analysis
Interface:
Command line interface
Input data:
An annotated long read sequence and short sequence tags.
Operating system:
Unix/Linux
Computer skills:
Advanced
Maintained:
No

CPTRA distribution

versioning

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No versioning.

CPTRA support

Maintainers

This tool is not available anymore.

Credits

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Publications

Institution(s)

Institute of Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA; State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China; Monsanto Co., Saint Louis, MO, USA; Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA; Department of Crop Sciences, University of Illinois, Urbana Champion, IL, USA; Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA

Funding source(s)

Supported by Texas Agrilife Research and Monsanto Inc.

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