BayesPrism Gateway is online service that supports Web-based science through the execution of online computational experiments and the management of data. The items below are trying to answer qustions from the users.
Q: How should I prepare count matrix files for BayesPrism Gateway?
A: The input to BayesPrism consists of two input matrices which represent the raw read count in bulk samples and the single-cell RNA-seq reference which can be supplied as either cell-by-gene raw count matrix (Reference Data Type=count matrix) or user-generated cell state-by-gene expression profile (Reference Data Type=GEP). Our gateway allows the count matrix or GEP describing the scRNA-seq reference to be exported from other single cell packages, such as Seurat and CellRanger. The details of the data format for the input matrices are described in the input tab of the documentation.
Q: How should I do when I meet the computational failure in the BayesPrism Gateway?
A: Firstly, please make sure that the input data meet the requirements, which you can found in the input tab of the documentation.
Here are some common causes of computational failure.
(1). Wrong file format. For details, please check the input tab of this page.
(2). Reverse rows and columns when submitting a count matrix file. BayesPrism needs two count matrixes, both of which are coded with genes(rows) by samples(columns).
(3). The data you submit cannot be calculated by BayesPrism. Here are some requirements. a) Each row of the count matrix indicates one unique gene id, so the count matrices should have the same gene set in the bulk and the reference. b) Count matrices are not normalizable. c) At least 50 reads for each cell type are suggested. d) It is recommended that at least one non-tumor sample be included in the cell profile.
Q: Which browser works well with the BayesPrism Gateway?
A: We have tested in the Firefox, Google Chrome and Safari so far. For IE (version 10 or 11) and some version of Safari, you maybe have trouble showing sequence data in WashU genome browser. For Safari users, please read next Q&A.
Q: What should the Safari users be aware of?
A: By default, Safari unzips a zip file automatically when you download it. However BayesPrism results are compressed by the 'bgzip' command which is not compatiable with the Safari method. It would be probelmatic when you download BayesPrism results. Please disable this feature in Safari and then download the compressed results from BayesPrism Gateway.
Secondly, when you click the genome browser link, please use the Left-Click, don't use Right-Click menu and the menu option "open a new tab".
Q: How long do my data and results keep in the BayesPrism Gateway?
A: One month.
Q: Do I have to create account before using this service?
A: Yes, this system is supported by an NSF funded supercomputing resource known as ACCESS, who regularly needs to report bulk usage statistics to NSF. Nevertheless, data that you provide are completely safe.
Q: How do I know the status of the computational nodes?
A: Since we can't update this web site very often, the gateway status is updated here on the BayesPrism page based on the notifications of the ACCESS community.
Q: Who do I thank for the computing power?
A: This web-based tool is powered by SciGaP and Apache Airavata and the GPU servers are supported by the ACCESS.
Q: I have another question that is not on this FAQ. How can I contact you?
A: Yes, please contact us with any questions! TinyiChu ( tc532@cornell.edu ).