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Xenome--a tool for classifying reads from xenograft samples.
Bioinformatics. 2012 Jun 15;28(12):i172-i178
Authors: Conway T, Wazny J, Bromage A, Tymms M, Sooraj D, Williams ED, Beresford-Smith B
Abstract
MOTIVATION: Shotgun sequence read data derived from xenograft material contains a mixture of reads arising from the host and reads arising from the graft. Classifying the read mixture to separate the two allows for more precise analysis to be performed.
RESULTS: We present a technique, with an associated tool Xenome, which performs fast, accurate and specific classification of xenograft-derived sequence read data. We have evaluated it on RNA-Seq data from human, mouse and human-in-mouse xenograft datasets.
AVAILABILITY: Xenome is available for non-commercial use from http://www.nicta.com.au/bioinformatics
CONTACT: [email protected].
PMID: 22689758 [PubMed - in process]
More...
Xenome--a tool for classifying reads from xenograft samples.
Bioinformatics. 2012 Jun 15;28(12):i172-i178
Authors: Conway T, Wazny J, Bromage A, Tymms M, Sooraj D, Williams ED, Beresford-Smith B
Abstract
MOTIVATION: Shotgun sequence read data derived from xenograft material contains a mixture of reads arising from the host and reads arising from the graft. Classifying the read mixture to separate the two allows for more precise analysis to be performed.
RESULTS: We present a technique, with an associated tool Xenome, which performs fast, accurate and specific classification of xenograft-derived sequence read data. We have evaluated it on RNA-Seq data from human, mouse and human-in-mouse xenograft datasets.
AVAILABILITY: Xenome is available for non-commercial use from http://www.nicta.com.au/bioinformatics
CONTACT: [email protected].
PMID: 22689758 [PubMed - in process]
More...