The "Demultiplexing from RUNID" pipeline divides the reads among the samples, and prepares FASTQ files for each sample.

Pipeline website: http://utap.wexac.weizmann.ac.il

Before you start:

This pipeline runs on the Wexac cluster. 
Please prepare the following in advance:

1. An account (userID) on Wexac, via your department administrator.
2. 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).
3. Sufficient free storage space on Wexac (> 400Gb), via your department administrator.

Setting up a new analysis

Note: This pipeline is only for users whose sequencing was done at the WIS Sandbox unit and hence have bcl files on the Stefan server. Need to check - Jordana/Michal

The pipeline copies the bcl files from the Stefan server into your Collaboration folder on Wexac, converts them to fastq files, and demultiplexes the fastq files according to the selected MARS-Seq or TruSeq (default) protocol.

You need to supply only the run id of your sequencing run (e.g.: 170802_NB501465_0140_AH3W3KBGX3). You can find this id in the email that you receive upon completion of the sequencing run.

Click on Demultiplexing_from_RUNID in the Choose pipeline box:

• Fill in your Stefan server run ID.  At the beginning of the analysis, your specified run ID's bcl files will be copied from Stefan.
• Fill in your samples names and barcodes by copying them from an excel file. The names cannot contain spaces or any of the listed invalid characters.
• Finally, submit the run for analysis.  

At the end of the run, a folder containing your samples' fastq files will be created in the Output folder that you specify.

/** What about dual barcode (index)? */

List of links 

Transcriptome pipeline for Weizmann Institute users:  http://utap.wexac.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

Visit our web site http://www.weizmann.ac.il/LS_CoreFacilities/bioinformatics-lscf/about)