RNA Seq Data Analysis by using the Galaxy platform

Dr Beáta Scholtz and Balint L. Balint, University of Debrecen

Galaxy is an open source, web-based platform for data intensive biomedical research (more info here: https://usegalaxy.org/). Galaxy is accessible on various servers word-wide for academic researchers.
RNA Sequencing is one of the most frequently used method to charachterize the transcriptional status of a cell or a system. Galaxy provides a straightforward, GUI (Graphical User Inferface) based access to a wide series of bioinformatic programs needed for genomic investigations.
The Course is part of a longer series of bioinformatic training events that covers various topics from very basics of bioinformatics and GUI based tools to unix based programs and R programming. 
This course is funded through the Debrecen Venture Catapult Program (EFOP-3.6.1-16-2016-00022) implemented through the New Hungary Development Plan co-financed by the European Social Fund and the European Regional Development Fund. 
Trainer of the course is Dr Beata Scholtz.
The course is free but registration is mandatory.
The language of the course is English. This will be a two days, hands on computer course. Zero prior bioinformatic knowledge is needed. 
We inviting life science researchers who are dealing with genomic datasets and would like to understand basic concepts of NGS data analysis.
The course will be run on local computers while Galaxy itself runs on servers, in this case our server. 
Venue: This is a computer room of the Medical Faculty located in the Dean's Office Building Shared with the International Student Coordination Center. The place can be easily accessed by Tram no 1, "Egyetem tér" station.  This building is on the left of the main building, the second building on the left of the university church. (On GoogleMaps is called OEC Erasmus Office)
GPS coordinates: 47°33'16.3"N 21°37'26.4"E, alternative format: 47.554517, 21.624006
We plan to provide coffee and refreshments including a sandwich lunch. 
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By the end of the course attendees should understand basic steps of NGS data analysis on RNA Seq and CHIP-Seq datasets. 
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We can not provide you lodging but if needed use booking.com for your convenience. 
Programme:
2018. 11. 17.  Saturday
 
9:30-10:00 Coffee and Welcome!
 
10:00-12:00 
Introduction to Galaxy.  Loading data into Galaxy from different sources.  Quality assessment: FASTQC (Colon cc data). Data preprocessing-quality correction: Trimmomatic.  Alignment to reference sequence.
 
12:00-13:00 Lunch break
 
13:00- 15:00 
Post-alignment quality control.  Build a workflow. Transcript and gene level differential expression.  
 
15:00-15:30 Coffee break
 
15:30-17:00
Transcript and gene level differential expression (continued).
 
2018. 11. 18.  Sunday
 
9:00-10:00
Transcript and gene level differential expression (continued).
 
10:00-10:30 Coffee break
 
10:30-12:30
Mutation analysis of RNAseq data.  Peeking out of Galaxy: annotation of mutations (VEP).  
 
12:30-13:30  Lunch break
 
13:30-14:30
Visualization of aligned data in Integrated Genomic Viewer.  Single nucleotide variant quality assessment in IGV. Transcript assembly visualization in IGV (Sashimi plot). 
 
14:30-15:00 Coffee Break
 
15:30-17:00 
ChIP-seq data analysis in Galaxy.

RNA Seq Data Analysis by using the Galaxy platform

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RNA Seq Data Analysis by using the Galaxy platform

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