Schedule

All posted times are Pacific time zone. At least one break will be provided each morning and afternoon.

Wednesday, September 30

8:50 am Zoom session starts
9:00 am Welcome, format and expectations, introductions
9:30 am Logging in to the cluster (hands on) Hannah
10:00 am Introduction to the command line / Advanced command line (hands on) Hannah / Nik
12:00 pm Lunch
1:00 pm Introduction to the command line / Advanced command line (hands on) Hannah / Nik
1:30 pm Clusters and modules (lecture and hands on) Hannah
2:00 pm PacBio Iso-Seq method and Library Prep Kristin Mars, PacBio
3:15 pm Examining PacBio data (lecture and hands on) Matt
5:00 pm Zoom session ends

Thursday, October 1

8:50 am Zoom session starts
9:00 am Review of previous day’s material Hannah
9:30 am Introduction to PacBio SMRT sequencing technology and the Iso-Seq method (lecture) Dr. Liz Tseng, PacBio
10:00 am Official PacBio software SMRT Analysis / BioConda (lecture) Dr. Liz Tseng, PacBio
10:30 am Iso-Seq pipeline with Bioconda and visualization using UCSC and IGV (hands on) Dr. Liz Tseng, PacBio
11:00 am Cupcake (hands on) Dr. Liz Tseng, PacBio
12:00 pm Lunch
1:00 pm Special Iso-Seq topic: Phasing and Cogent (lecture and hands on) Dr. Liz Tseng, PacBio
2:00 pm Special Iso-Seq topic: Single Cell Iso-Seq (lecture and hands on) Dr. Liz Tseng, PacBio
3:15 pm TAMA (lecture) Richard Kuo, Roslin Institute, University of Edinburgh
3:45 pm TAMA (hands on) Richard Kuo, Roslin Institute, University of Edinburgh
4:45 pm Homework: check tappAS installations Bioinformatics Core
5:00 pm Zoom session ends

Friday, October 2

8:50 am Zoom session starts
9:00 am SQANTI (lecture) Dr. Lorena de la Fuente, developer, SQANTI
9:30 am SQUANTI (hands on) Francisco Pardo Palacios, Universitat Politècnica de València
10:30 am IsoAnnot and IsoAnnotLite (lecture) Francisco Pardo Palacios, Universitat Politècnica de València
11:00 am IsoAnnot and IsoAnnotLite (hands on) Francisco Pardo Palacios, Universitat Politècnica de València
12:00 pm Lunch
1:00 pm tappAS (lecture) Dr. Ana Conesa, University of Florida
2:00 pm tappAS (hands on) Ángeles Arzalluz-Luque, Universidad Politécnica de Valencia
4:00 pm Experimental design and closing thoughts (lecture) Matt
5:00 pm Zoom session ends