bioRxivBioinformaticsPreprint
XenoCP: Cloud-based BAM cleansing tool for RNA and DNA from Xenograft
Michael RuschiD, Liang DingiD, Sasi ArunachalamiD, Andrew ThrasheriD, Hongjian JiniD, Michael MaciasiD, Lawryn H. Kasper, André Bortolini SilveiraiD, Michael A. DyeriD, Suzanne J. BakeriD, Jinghui ZhangiD
Abstract
SummaryXenografts are important models for cancer research and the presence of mouse reads in xenograft next generation sequencing data can potentially confound interpretation of experimental results. We present an efficient, cloud-based BAM-to-BAM cleaning tool called XenoCP to remove mouse reads from xenograft BAM files. We show application of XenoCP in obtaining accurate gene expression quantification in RNA-seq and tumor heterogeneity in WGS of xenografts derived from brain and solid tumors. Availability and ImplementationSt. Jude Cloud (https://pecan.stjude.cloud/permalink/xenocp) and St. Jude Github (https://github.com/stjude/XenoCP)
- organism: mouse
- organism: human
- assay: DNA methylation
- assay: whole-genome sequencing
- assay: bulk RNA-seq
- research focus: variant calling
- research focus: gene regulatory network inference
- research focus: software / tool
- approach: experimental assay
- Citations
- 4
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