SUSHI monthly seminars in 2024
Participants limit (max in each session): 250
| Date Year 2024 | Topics | Main presenters | Registration | |
| 29 Mar. 10:00- | FastQC + Kallisto + CountQC (A typical RNAseq workflow) | MH slides | Please contact masaomi.hatakeyama@uzh.ch | |
| 26 Apr. | SUSHI course instead of seminar (See below in detail) | MH | Please contact courses@fgcz.ethz.ch | |
| 29 May 14:00- | A typical scRNAseq workflow (cellRanger + Seurat) | PG | ||
| Jun. | Interactive bulk/single-cell RNA Seq Analysis in Shiny | PL | ||
| July-Aug. | Summer break | |||
| Sep. | Cell type identification for single-cell RNA-seq data in SUSHI | HR | ||
| Oct. | Genome Informatics Workshop | |||
| Nov. | Spatial Transcriptomics Analysis via Sushi | LO | ||
| Dec. | A typical metagenomics workflow (QIIME2/Mothur+Phyloseq) | NZ | ||
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: 26, April, Fri, 2024
- morning: lecture + demo, afternoon: practicals + QA session
- To register for SUSHI course, please contact courses@fgcz.ethz.ch
- https://fgcz.ch/education/bioinformaticsTraining/NGSintroSushi.html
SUSHI SWITCHcast channel
- https://uzh.mediaspace.cast.switch.ch/channel/SUSHI+seminar
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
- 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
- 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)
- 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 2023
Participants limit (max in each session): 250
| Date Year 2023 | Topics | Main presenters | Registration | |
| 17 Mar. Fri, 14:00-15:00 | FastQC + Kallisto + CountQC (A typical RNAseq workflow) | MH slides video | closed | |
| Apr. | Canceled | |||
| 26 May Fri, 14:00-15:00 | A typical RNAseq workflow (edgeR and/or DESeq2) | AG slides video | closed | |
| 30 June Fri. 14:00-15:00 | Interactive Bulk RNA Seq Analysis in Shiny | PL video | closed | |
| July-Aug. | Summer break | |||
| 29 Sep. Fri., 14:00-15:00 | Cell type identification for single-cell RNA-seq data in SUSHI | HR slides video | closed | |
| 27 Oct. Fri., 14:00-15:00 | Genome Informatics Workshop | |||
| Nov. | Spatial Transcriptomics Analysis via Sushi | LO | Canceled | |
| Dec. | A typical metagenomics workflow (QIIME2/Mothur+Phyloseq) | NZ | Canceled | |
SUSHI monthly seminars in 2022
Participants limit (max in each session): 250
| Date Year 2022 | 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 | |
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 | ||