January 16th, 2018 : Introduction to the HPC
This week we will discuss the UCI High Performance Computing Cluster (HPC). Please visit the HPC website to set up your account and familiarize yourself with this resource. An account will be helpful to follow along with the session.
January 23rd, 2018: Working on the HPC
This week we will discuss how to use the UCI HPC. We will look at the basic anatomy of a bash script and use the modules available on the HPC to do simple tasks.
January 31th, 2018: Getting Data
This week we will discuss how to transfer your data to and from the HPC. We will also introduce you to the NCBI Sequence Read Archive (SRA) as one resource for publicly available data.
February 7th, 2018: FastQC Analysis
This week we will go over how to look at the quality of your data using FastQC from the command line. We will review what your data looks like and what it all means!
February 14th, 2018: Getting Ready for Analysis
This week we will discuss how to prepare for sequence analysis by getting the proper files (eg genome indices, gene feature files). We will also discuss possible file organization structures to help you stay organized throughout the process.
February 21st, 2018: NO MEETING
February 28th, 2018: Managing and Manipulating Files with Sed and Awk
This week we will have our first guest presenter! Dr. Anne Sonnenschein is a lecturer at Chapman University and will be discussing file manipulation using regular expressions and helpful tools like sed and awk.
March 7th, 2018: Trimming Data
This week we will discuss how to trim your data primarily using the program Trimmomatic. We will take the trimmed data's FastQC results and compare it to the FastQC results of the untrimmed data.
This week Kerrigan Blake and Nicholas Pervolarakis will discuss the use of task arrays, a mechanism for submitting and managing collections of similar jobs quickly and easily on the HPC.
March 21st, 2018: Sequence Alignment Programs
This week we will discuss how to map the reads from your experiment to a genome of interest using sequence alignment programs. We will review the different options for sequence alignment and focus on using STAR and HiSat2 to process our data.
March 28th, 2018: Recap/Review Session
This week we will go over any questions that you have from topics discussed in our previous meetings. If you have not been able to attend the meetings this past quarter but would like to start, this is an excellent opportunity to get caught up and ready for the upcoming weeks.
This week we will discuss the read counting program HTSeq.
April 11, 2018: Introduction to R
This week will introduce basic concepts of the programming language R and setup our laptops with R and RStudio.
April 18, 2018: Normalizing Data with Spike-ins
This week Elmira Forouzmand, a computer science graduate student, will discuss the ERCC spike-in and how it is used for normalization.
April 25, 2018: Intermediate R
This week Athit Kao will expand on R by introducing the concept of functions in R scripts.
May 9, 2018: Introduction to DESeq2
We will discuss the popular differential analysis program DESeq2 using R.
Dr. Weining Shen from the UCI Department of Statistics will discuss basic statistical approaches for data analysis and alternative options on campus for more complex analysis needs.
May 23rd, 2018: Data visualization with ggplot2
ROOM CHANGE: Sprague Basement conference room B002
This week Athit Kao will introduce the powerful R plotting package ggplot2.
May 30rd, 2018: CANCELLED
June 06, 2018: Introduction to ChIPseq
This week, Elmira Forouzmand will discuss ChIPseq data analysis including the Irreproducibility Discovery Rate (IDR) framework.
June 13, 2018: Metagenomic Data Analysis
Dr. Whitney England, a bioinformatician from the Spitale Lab, will discuss metagenomic data analysis.
September 26th, 2018: Introduction to Linux and the UCI HPC
October 3th, 2018: Introduction to Linux and the UCI HPC
This topic will be covered during two meetings (9/26/18 and 10/03/18). We will introduce the command line, basic commands in Linux, and will log on to the UCI High Performance Computing Cluster (HPC). Please fill out our RSVP form prior to the meeting. You must have an HPC account to log on to the UCI HPC, this will be provided for you if requested on the RSVP form.
October 10th, 2018: Bash Scripting and Working on the HPC
This week we will discuss the basic anatomy of a bash script and how to write a script specifically for running jobs on the UCI HPC.
October 24th, 2018: ATAC-seq/ChIP-seq workflow and data analysis
This week Dr. Mandy Jiang from the Mortazavi lab will present on the overall workflow for peaking calling computational methods. ATAC-seq and ChIP-seq methods will be discussed.
October 29th, 2018: Nanopore workflow and data analysis
This week Gabriela Balderrama Gutierrez from the Mortazavi lab will discuss the overall work flow and data analysis for Nanopore sequencing.
November 14th, 2018: UCI Genomics High-throughput Facility - Dr. Melanie Oakes
This week Dr. Melanie Oakes will discuss the services and technologies available at the UCI GHTF. Afterwards, we will have an open discussion for questions in regards to library preparation.
December 5th, 2018: Single Cell RNA-seq workflow and data analysis
Nick Pervolarakis from the Kessenbrock lab will discuss the overall workflow for single cell RNA-seq.
June 26th, 2019: Introduction to R
Meeting Information: Sprague 105, 2pm - 4pm
This is the first meeting of the Bioinformatics Support Group for Summer 2019. This week Stacey Borrego will introduce the basics of the programming language R using RStudio. Beginners are encouraged to attend! Please visit the presentation page to install R and RStudio prior to the meeting.
July 3rd, 2019: Open Work Session
Meeting Information: Sprague 105, 2pm - 4pm
This is our first Open Work Session! We look forwarding to hosting this session where everyone should feel free to come work on their projects and ask questions that they may be struggling with. Light snacks will be provided.
Setting up just the right combination of modules, packages, and OS environmental variables has been a major hurdle for running open-sourced bioinformatics pipelines on the HPC. In addition, pipelines increasingly require the use of novel visuals for interactive data exploration. To better meet these challenges, RCIC and GHTF have partnered to provide on the HPC, Singularity containerization for software environment virtualization, as well as JupyterHub for serving interactive computational notebooks and R Studio.
July 18th, 2019: Open Work Session
Meeting Information: Sprague 105, Thursday 2pm - 4pm
Feel free to join us for some dedicated work time. Work on your projects, ask questions, and enjoy some snacks!
July 25th, 2019: Data Visualization with R - Kevin Cabrera
Meeting Information: Sprague BASEMENT (take the elevator downstairs), Thursday 2pm - 4pm
This meeting will introduce basic concepts in R that will allow you to load, manipulate, and visualize data. R Packages of focus include those of the well-known Tidyverse, specifically ggplot2 and dplyr.
August 1st, 2019: Open Work Session
Meeting Information: Sprague BASEMENT (take the elevator downstairs), Thursday 2pm - 4pm
Feel free to join us for some dedicated work time. Work on your projects, ask questions, and enjoy some snacks!
August 8th, 2019: Introduction to Python - Conor Cox, PhD
Meeting Information: Sprague 105, Thursday 2pm - 4pm
This presentation will introduce some of the basics of running Python on your computer and will review a few datatypes in Python . To demonstrate Python in action, Conor will also provide a tutorial to write a simple VCF parser.