Copy of BBCU - NGS pipelines website (public)
First using:
For using with ngs-pipelines portal you need to create a Collaboration folder that has read-write permissions for the Bioinformatics Unit. This can be done with the help of the WEXAC IT (Hpc@weizmann.ac.il).
Now you can run analysis by the portal:
Login to http://ngsbio.wexac.weizmann.ac.il website with your user name and password of your Weizmann account.
In the portal there are two sections, User datasets, and Create analysis. There are links to them in the upper navigation bar:
1) User datasets: contains table with all the analysis of the user:
You can see the status of the run (RUNNING/SUCCESSFOL/FAILES). You need refresh the page to see if the status is changed (you also will get email in the end of the run).
2) Create Analysis:
You have three pipelines (for now):
1) Demultiplexing form run_id:
You can use with this pipeline If you did the sequencing in Sandbox unit.
The pipeline copy the bcl files from Stefan server into your Collaboration folder on wexac server, convert it to fastq files, and demultiplexes the fastq file according MAR-seq or True-seq (or semi- True-seq) protocol.
You need supply only the run id of your sequencing run (something like: 170802_NB501465_0140_AH3W3KBGX3). You can find this id in the email on the end on the sequencing run.
2) Demultiplexing form BCL files:
Create folder in
- If you have bcl files copy them to wexac server: under the Collaboration folder create sub-folder and copy to there the bcl folder.
You need copy all original folder of the bcl files as it written by Next-seq (or Hi-seq) machine. The folder name need to look like this name: "170802_NB501465_0140_AH3W3KBGX3"
for example /home/labs/USER_LAB/Collaboration/Project1/170802_NB501465_0140_AH3W3KBGX3 - The output will be writen to /home/labs/USER_LAB/Collaboration/Project1 folder
The pipeline convert bcl files to fastq files and demultiplexes the fastq file according MAR-seq or True-seq (or semi- True-seq) protocol.
In the portal, you need to choose the bcl folder:
3) Demultiplexing form fastq files:
The pipeline demultiplexes the fastq file according MAR-seq or True-seq (or semi- True-seq) protocol.
1.You need copy fastq files to wexac server: under the Collaboration folder create sub-folder and copy to there the fastq files.
- for example /home/labs/USER_LAB/Collaboration/Project1/*R1.fastq*
- The output will be writen to /home/labs/USER_LAB/Collaboration/Project1 folder
In the portal, you need to choose the fastq files from the list.
If the sequencing is single read, choose for read 1 the file with *R1* in its file name, and for index read the file with *R2* (sometimes it is called *I1*), and remain empty the field of read 2.
If the sequencing is paired end, choose for read 1 the file with *R1* in its file name, and for read 2 the file with *R2*, and for index read the file with *I1*. If have no file with *I1* name, choose *R2* file for index read and *R3* file for read 2.
