Data Therapy Archive 2017
Data Therapy Week – 01 : Introduction to the CBC and the resources
Feb 3rd 2017
DataTherapy_Week01
CBC Open House 2017
Friday, 24th of February at Grossman Auditorium, Cell and Genome Science Building, UConn Health Center. [schedule]
Data Therapy Week – 02 : Discussion on Databases
Data Therapy Week – 03 : Genome Assembly
Friday March 3rd at 10.00 am in BioPharm 203
Discussed ideal sequencing strategies for de-novo genome assembly of Non-model species.
Discussed genome assembly tools/softwares e.g.: MaSuRCA, Allpaths, SOAPdenovo2, SPAdes
What type of sequencing data is better when you are doing a population studies?
How to go about doing assembly when you have RAD-seq data.
Data Therapy Week – 04 : RADSeq
Friday, March 24th at 10:00 am in BioPharm 203.
Data Therapy Week – 05 : ChIP-Seq
Friday, April 7th at 10:00 am in BioPharm 203.
Data Therapy Week – 06 : Introduction to HPC Resources
Friday, April 21st at 10:00 am in BioPharm 203.
- BBC cluster and it's different nodes
- How to open a graphical terminal to display (pdf and image files)
- In the cluster working directory (or in Home directory), using a terminal type: python -m SimpleHTTPServer
- In a new terminal using your PC/lap-top run: ssh -NL 8000:localhost:8000 <user_name>@bbcsrv3.biotech.uconn.edu , and leave the terminal window open.
- Then open a browser window in your computer and type: http://localhost:8000 to view your working directory and to open pdf and image files.
- How to submit a single job and a array job using qsub
- Data transfering
Data Therapy Week – 07 : RNA-Seq
Friday, May 5th at 10:00 am in BioPharm 203.
- RNA-Seq versus Microarrays
- RNA-Seq workflow
- Designing the Study
- Paired versus Single-End
- Analysis Challenges
- One Gene: Two Isoforms: Opposite Functions
- Quality Control
- Read Mapping or Assembly
- Generating Raw Reads
- Differential Expression
Data Therapy Week – 08 : Metagenomics
Friday, May 19th at 10:00 am in BioPharm 203.
- General workflow
- Resources ( 16S / Genomes / Metagenomes / Function )
- General Challenges / Considerations
- Marker Genes
- Bioinformatics workflow
Data Therapy Week – 09 : HPC Basics and Introduction to Xanadu Cluster
Friday, June 2nd at 10:00 am in R1401 Cell and Genome Science Building - Farmington, CT
- Introduction to High Performance Computing
- A Typical HPC cluster
- Connecting to Xanadu Cluster
- Common Linux Commands
- Software on the Cluster and How to Access
- Composing a (SLURM) Script for Xanadu Cluster
CBC_DataTherapy_HPC_Xanadu_Introduction_Week09
Data Therapy Week – 10 : Metatranscriptomics
Friday, June 16th at 10:00 am at BioPharm 203 - Storrs CT
- Focus of Metatranscriptomics:
- Common RNA Seq techniques
- Challengers
- Typical Analytical Pipeline
- Read or Transcript Processing
- Visualizing Results
Data Therapy Week – 11 : Introduction to Xanadu HPC (Storrs)
Friday, June 30th at 10:00 am at BioPharm 203 - Storrs CT
- Introduction to the Xanadu Cluster
CBC_DataTherapy_HPC_Xanadu_introduction (Download .ppt)
Data Therapy Week – 12 : RNA-Seq Challenges
Friday, July 14th at 10:00 am at BioPharm 203 - Storrs CT
Data Therapy Week – 13 : Introduction to Unix and HPC with Xanadu!
Friday, July 28th at 10:00 am at BioPharm 203 - Storrs CT
Data Therapy Week – 14 : Introduction to Linux (Basics)
Friday, August 11th at 10:00 am at BioPharm 203 - Storrs CT
Data Therapy Week – 15 : Introduction to Linux (How to write scripts)
Friday, September 8th at 11:30 am at Engineering Science Building (ESB) 205 - Storrs CT
-How to write a simple script
-How to use it for multiple files
-How to use it with command line variables
Demonstration
Data Therapy Week – 16 : FASTQC: Quality Control of FASTQ Files
Friday, September 22nd at 10:30 am at Engineering Science Building (ESB) 304 - Storrs CT
FASTQC
Evaluating the quality of reads using FASTQC - before and after trimming
Demonstration
Data Therapy Week – 17 : Illumina Read Processing
Friday, October 6th at 10:30 am at Engineering Science Building (ESB) 304 - Storrs CT
Processing of Illumina Reads
Read trimming tools: Sickle, Cutadapt and Trimommatic
Demonstration
Data Therapy Week – 18 : Consultation
Friday, at 10:30 am at Engineering Science Building (ESB) 304 - Storrs CT
Discussion of research problems to address individual needs.
Data Therapy Week – 19 : Consultation
Friday, November 3rd at 10:30 am at Engineering Science Building (ESB) 304 - Storrs CT
Discussion of research problems to address individual needs.
Please come and discuss your research with us.
Data Therapy Week – 20 : Genome Size Estimation
Friday, November 17th at 10:30 am at Engineering Science Building (ESB) 304 - Storrs CT
Genome size estimation using K-mer method
Data Therapy Week – 21 : RNA-Seq
Friday, December 1st at 10:30 am at Engineering Science Building (ESB) 304 - Storrs CT
Data Therapy Week – 22 : HPC with Xanadu
Friday, December 15that 10:30 am at Engineering Science Building (ESB) 304 - Storrs CT