16.2.22 UTAP: Demultiplexing from BCL pipeline guidelines

Owned by Jordana Lindner
Last updated: 16 Feb, 2022
2 min read

The Demultiplexing from BCL pipeline /** MORE **/

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

  1. If you have bcl files, copy them to a subdirectory (folder) of your wexac server's Collaboration folder, say called Project1.
    You must copy the entire original bcl files folder as written by the Next-seq (or Hi-seq) machine.
  2. The folder's name must conform to the following pattern: <part1>_<part2_<part3>, where <part1> corresponds to /* ?? */, <part2> corresponds to /* ?? */, and <part3> corresponds to /* ?? */   - (e.g. "170802_NB501465_0140_AH3W3KBGX3", with the full path of  /home/labs/<USER_LAB>/Collaboration/Project1/170802_NB501465_0140_AH3W3KBGX3)
  3. The output will be written to the  /home/labs/USER_LAB/Collaboration/Project1 folder /** where in the folder? Perhaps in an output subdir of 170802_NB501465_0140_AH3W3KBGX3 - or a general output subdir of the parent? **/

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:

The pipeline converts bcl files to fastq files and demultiplexes the fastq file according to either the MAR-seq or True-seq (or semi- True-seq) protocol.

Click on Demultiplexing_from_BCL in the Choose pipeline box:






/** Add Analysis workflow */

/* Output folders section? */


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

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