TRANSPOSABLE ELEMENT ANALYSIS PIPELINE

Welcome to the companion site for the Tea repeat analysis pipeline. Tea stands for transposable element analyzer. This site will serve as both a resource for downloading additional data related to the paper and as a repository for the Tea pipeline. The paper describing Tea is:

DOWNLOAD ADDITIONAL DATA FILES

DOWNLOAD Tea PIPELINE

The pipeline can be downloaded using the links provided below. Please see the included README file for instructions on running the pipeline. Installation requires the following software to be present on the system: the CAP3 assembler, Perl, R, Samtools and the BWA aligner software. The following R packages are also required: Bioconductor, Rsamtools, IRanges and spp. Currently, the only supported operating system is Linux on an x86 compatible architecture. The current version has limitations for supporting human reference hg19 and non-human genomes. The next version will handle hg19 and introduce additional features. We expect that it will be released fall 2013.

For the purposes of testing the pipeline we have included demo data files, containing chromosomes 21 and 22 from the three HapMap normal samples analyzed in the paper:

If you have any other questions about Tea, please contact Alice Lee (Alice Lee).

GET INVOLVED

A postdoctoral position in bioinformatics is available at the Kharchenko Lab. The candidate will work on development of algorithms and statistical methods for analyzing genomic and functional sequencing data, in close collaboration with experimental labs. Read more.