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asmariyaz23 edited this page Jul 18, 2018
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The Trinity Cancer Transcriptome Analysis Toolkit (CTAT) aims to provide tools for leveraging RNA-Seq to gain insights into the biology of cancer transcriptomes.
For foreign transcript detection, we leverage Centrifuge and Kraken, leveraging RNA-Seq reads and Trinity-reconstructed transcripts. Our efforts here are being carried out in collaboration with the group of Steven Salzberg at JHU.
- git clone https://github.com/NCIP/ctat-metagenomics.git
- Conda installation
- Galaxy toolshed installation of the tool
- Run this tool via our Trinity CTAT Galaxy Portal.
Contact us on our google group https://groups.google.com/forum/#!forum/trinity_ctat_users
Kim, D., Song, L., Breitwieser, F. P., & Salzberg, S. L. (2016). Centrifuge: rapid and sensitive classification of metagenomic sequences. Genome Research, 26(12), 1721–1729. https://doi.org/10.1101/gr.210641.116