16.2.22 UTAP: Cell Ranger pipeline for single cell mRNA (scRNA) gene expression (GEX)
Select the cellranger count pipeline from UTAP interface.
Currently the pipeline only supports the count command and the aggregation of samples.
Pipeline website: http://utap.wexac.weizmann.ac.il
Before you start:
This pipeline runs on the Wexac cluster.
Please prepare the following in advance:
- An account (userID) on Wexac, via your department administrator.
- A "Collaboration" folder within your lab folder on Wexac, with read and write permission for Bioinformatics Unit staff. This must be set up by the computing center (hpc@weizmann.ac.il).
- Sufficient free storage space on Wexac (> 400Gb), via your department administrator.
Setting up a new analysis
In order to run a new transcriptome analysis, you must first transfer demultiplexed sequencing data (fastq files) to your Collaboration folder.
Then, login to utap.wexac.weizmann.ac.il via Firefox or Chrome (the pipeline is NOT compatible with Internet Explorer) using your Weizmann userID and password, and click on Run pipeline:
Click on Singlecell Cellranger in the Choose pipeline box:
Selecting Input folder: Within the cellranger demultiplexed outputs, select the folder above the outs folders (under outs is the fastq_path folder).
Cellranger genome: Choose the relevant genome from the drop-down list.
/** Add Analysis workflow */
/* Output folders section? */
Caveats:
- Use NovaSeq only with unique dual indexing pooling combinations (unique i5 and i7 indexes). Index hopping (or index switching) is a known phenomenon in NovaSeq. It causes incorrect assignment of libraries from the expected index to a different index (in the multiplexed pool). For some protocols (e.g. 10X Genomics), scRNA-Seq index hopping contaminations can be eliminated by using bioinformatics procedures. Please consult with us at utap@weizmann.ac.il
- Please note that Single Cell Cellranger requires significant machine resources. Depending on WEXAC's load, it might take up to several days for your results to arrive.
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