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SUSHI monthly seminars in 2022


Participants limit (max in each session): 250

Date Year 2021 Topics Main presenters Registration
18 Mar. Fri, 14:00-15:00 FastQC + Kallisto + CountQC (A typical RNAseq workflow) MH slides video closed
Apr. Canceled
17 May Tue, 14:00-15:00 A typical RNAseq workflow (edgeR and/or DESeq2) AG slides video closed
23 June, Thu 14:00-15:00 Interactive Bulk RNA Seq Analysis in Shiny PL video closed
July-Aug. Summer break
30 Sep., Fri. 14:00-15:00 Aspects of read mapping HR slides video closed
28 Oct, Fri. 14:00-15:00 A typical SNP calling workflow (DNA, GATK) LO slides video closed
Nov. Canceled
16 Dec., 14:00-15:00 A typical metagenomics workflow (QIIME2/Mothur+Phyloseq) NZ slides video closed


What is SUSHI?
- SUSHI is an integrated framework of NGS data analysis designed and developed at FGCZ, similar to Galaxy, CLC workbench.
- All sequenced NGS data are transferred to a file server and SUSHI system at FGCZ and subsequently quality control jobs are automatically executed, and the graphical reports are generated.
- All BFabric users can access SUSHI: https://fgcz-sushi.uzh.ch

Note
- This seminars focus only on the usage of SUSHI, rather than the background theories/technologies of NGS data analysis
- The slides and practical are reused/recycled from/to other bioinformatics courses at FGCZ.

SUSHI one-day crash course
- Date: 24, June, Fri, 2022
- morning: lecture + demo, afternoon: practicals + QA session
- To register for SUSHI course, please contact courses at fgcz.ethz.ch
- https://fgcz.ch/education/bioinformaticsTraining/NGSintroSushi.html

SUSHI SWITCHcast channel
- https://uzh.mediaspace.cast.switch.ch/channel/SUSHI+seminar+2022/12795

References/useful links
- https://github.com/uzh/sushi
- https://github.com/uzh/ezRun

Quesion?
- First please look at the FAQ section below whether the same/similar question has already asked or not.
- Then, if not, please contact Masa


FAQ


How can I change/edit the sample information of the DataSet table?

A: At the DataSet veiw, click edit table link and subsequently click edit table content button. save button overwrites the current DataSet, and save as child creates a new DataSet with keeping the original DataSet.

How can I integrate/merge two DataSets from different projects?

A: Please follows the steps below

  1. Download the DataSet table as a tsv file to your local computer (laptop) by clicking download link and Download dataset description table link in the popup window
  2. Merge them with being careful of the column name (e.g. by MS Excel, or text editor) and save it as .tsv (Tab-Separated-Values) format (text file)
  3.  From import menu of the top, you can import it in your project

Note
  • The result DataSet from the merged DataSet will be produced under the selected project

Is it possible to upload my own data (externally sequenced not at FGCZ) to SUSHI?

A: Yes, it is possible, but there is no function in SUSHI to do it. Please contact us first and send your data. We will upload it to SUSHI. It will be charged depending on the data size. Please contact us for more details.

How long is the data kept in SUSHI/FGCZ?

A: A project must be finished basically in 3 years. The raw sequenced data (delivery-only) will be removed from our server basically in one month and it will be archived. The calculated data in SUSHI will be kept basically until the project ends, except for tremendously huge data.

How can I exclude/select samples for a job in the parameter setting view?


A: In the parameter setting view of the application, samples field is selectable. You can select the samples that you want to use for the application, by SHIFT/CTL + click. By default, all the samples are selected.

SUSHI monthly seminars in 2021


Participants limit (max in each session): 250

Date Year 2021 Topics Main presenters Registration
19 Mar. Fri, 14:00-15:00 FastQC + Kallisto + CountQC (A typical RNAseq workflow) MH slides closed
23 Apr. Fri, 14:00-15:00 A typical RNAseq workflow (edgeR and/or DESeq2) AG slides closed
28 May, Fri. 14:00-15:00 A typical scRNAseq workflow DG slides closed
25 Jun., Fri. 14:00-15:00 A typical SNP calling workflow (DNA, GATK) LO slides closed
July Summer break NA
27 Aug., Fri. 14:00-15:00 Aspects of read mapping HR slides closed
24 Sep., 14:00-15:00 Interactive Bulk RNA Seq Analysis in Shiny PL slides closed
xx Oct., 14:00-15:00 TBD TBD
xx Nov., 14:00-15:00 TBD TBD
xx Dec., 14:00-15:00 TBD TBD




Created by masaomi. Last Modification: 2023-01-12 09:23 by masaomi.