UTAP requirements, setup, and reports (Weizmann users)
UTAP: User-friendly Transcriptome Analysis Pipeline
In order to run a transcriptome analysis, your lab must have:
- An account on Wexac
- Sufficient free storage space (> 400Gb)
- A "Collaboration" folder within your lab folder, with read and write permissions for the LSCF (Life Science Core Facility) Bioinformatics Unit
Requirements 1 and 2 can be set up by your department secretary or administrator. Requirement 3 must be set up by the computing center (contact hpc@weizmann.ac.il).
Running analyses in the portal:
After completing all of these UTAP setup requirements,
login to the http://utap.wexac.weizmann.ac.il website with the user name and password of your Weizmann account.
In the portal there are three sections: User Datasets, Upload data and Run pipeline, with links to them in the upper navigation bar as shown below:
1) User Datasets: contains a table with all of the available information about the user's analysis runs.
This includes the name, status of each run (RUNNING/SUCCESSFUL/FAILED), the relevant pipeline, and the date/time of when the run was created.
Refresh the page to see if any of the statuses has changed. In addition, email is sent at the end of each run.
2) Run pipeline:
The following pipelines are supported, please select for further information:
1,2) Transcriptomes from RNA-Seq and MARS-Seq
3) Demultiplexing from BCL files
4) ATAC-Seq
5) ChIP-Seq
6) Single-cell RNA Cell Ranger
List of links
Transcriptome pipeline for Weizmann Institute users: http://utap.wexac.weizmann.ac.il
Demo of the UTAP interface (for internal and external users): http://utap-demo.weizmann.ac.il
Acknowledgments
Citation:
Kohen et al. BMC Bioinformatics (2019) 20:154 https://doi.org/10.1186/s12859-019-2728-2 (PMID: 30909881)
Bioinformatics support staff for UTAP:
- UTAP development and maintenance team: utap@weizmann.ac.il
- Dena Leshkowitz
- Ester Feldmesser
- Gil Stelzer
- Bareket Dassa
- Noa Wigoda