Title

Authors

Affiliation

Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610

Email

jiqiangyao@ufl.edu; *Corresponding author

Article Type

Web Server

Date

Received July 30, 2011; Accepted July 31, 2011; Published August 20, 2011

Digital expression (DE) is an important application of RNA-seq technology to quantify the transcriptome. The number of mapped reads to each transcript or gene varies under different conditions and replicates. Currently, three different statistical algorithms (edgeR, DESeq and bayseq) are available as R packages, to compare the reads to identify significantly expressed transcripts or genes. So far, users have to manually install and run each R package separately. It is also of users’ interest to compare the results of different approaches. Here, we present a pipeline DEB which automates all the steps in file preparation, computation and result comparison.

Keywords

DEB, edgeR, DESeq, baySeq, RNA-seq, digital expression, nextGen sequencing

Availability

http://www.ijbcb.org/DEB/php/onlinetool.php

Citation

Yao & Yu. Bioinformation 7(1): 44-45 (2011)
 

Edited by

P Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.