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In order to run a transcriptome analysis, your lab must have:
An account on Wexac
Sufficient free storage space (> 400Gb)
Requirements 1 and 2 can be set up by your department secretary or administrator.
3. A "Collaboration" folder within your lab folder, with read and write permissions for the LSCF (Life Science Core Facility) Bioinformatics Unit.
Must be set up by the computing center (contact hpc@weizmann.ac.il).
4. Input data folders in the Collaboration folder with a required structure.
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The required read files for each protocol are detailed in the table below:
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NOTES:
SE- single end, PE- paired end.
Illumina compatible protocols refer to all protocols that have the barcode in the adaptors, including: RNA-Seq, ChIP-Seq, ATAC-Seq & Ribo-Seq.
Files structure example:
root_folder
sample1
sample1_R1.fastq
sample1_R2.fastq
sample1_R3.fastq
sample2
sample2_R1.fastq.gz
sample2_R2.fastq.gz
sample2_R3.fastq
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In the portal there are four sections: e-learning, User Datasets, Upload data and Run pipeline, with links to them in the upper navigation bar as shown below:
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e-learning: contains a link to interactive e-learning modules (for RNA-Seq & MARS-Seq) with detailed explanations of the library structure, pipeline analysis & report components.
The module also includes instructions how to run the pipeline.
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3) ATAC-Seq
4) ChIP-Seq
5) Ribo-Seq
6) Demultiplexing from BCL files
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8) Demultiplexing from FASTQ (need to add a page)
List of links
Pipeline website for Weizmann Institute users: https://utap.wexac.weizmann.ac.il/
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UTAP development and maintenance team: utap@weizmann.ac.il
Dena LeshkowitzEster Feldmesser
Gil Stelzer
Bareket Dassa
Noa Wigoda
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