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      PacBio Iso-Seq Workshop Online

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Introduction
Intro to the Workshop
Schedule
Support
Using Slack in this workshop
Using Zoom in this workshop
Cheat Sheets
Software and Links
Talks
Perspective on Bioinformatics/Genomics?
Iso-Seq Library Prep
Command Line Interface
Logging In and Transferring Files
Intro CLI
Advanced CLI
Advanced CLI Challenge Solutions
Clusters and Modules
Data Reduction
PacBio data
Dr. Liz Tseng
SMRT Sequencing - How it Works
Using the Iso-Seq Application on SMRT Link and BioConda
IsoPhase - Isoform-Level Phasing
Single-Cell RNA Sequencing using the Iso-Seq Method
Tutorial
Richard Kuo
Transcriptome Annotation by Modular Algorithms TAMA
TAMA (hands-on)
Tutorial
Conesa Lab
Installing tappAS
Quality Control and Characterization of LR Transcriptomes
SQANTI3 hands on and IsoAnnot
Hands-on tappAS
ETC
Closing thoughts
Workshop Photos
Github page
Biocore website
Pacific Biosciences website
Conesa lab website

TAMA (hands-on)

Richard Kuo, Roslin Institute, University of Edinburgh

Remember to run these commands to obtain the data and files for TAMA

cd /share/workshop/isoseq_workshop/$USER/
cp /share/workshop/isoseq_workshop/rkuo/folder_copy.tar.gz .
tar -xzvf folder_copy.tar.gz
git clone https://github.com/GenomeRIK/tama.git

Load modules

module load samtools/1.10 bedtools2/2.29.2 biopython/1.71 bamtools/2.4.2 minimap2/2.17

Click here for the rest of the TAMA Tutorial we’ll be following today. Start at the beginning where the header is labeled ‘UC Davis TAMA Tutorial 1.’

Now, we’ll move onto ‘UC Davis TAMA Tutorial 2.’

Copy and paste these files into your browser, and it should prompt you to download them onto your computer so we can view them on IGV

ftp://ftp.ed.ac.uk/edupload/map_cds_tc_nc_nolde_mm2_alz_flnc_hg38.bed
ftp://ftp.ed.ac.uk/edupload/tm_tc_flnc_nolde_gencode_100.bed

We’ll be viewing them in the IGV web app here. Make sure it’s loaded in hg38 like earlier. Then, load the two ftp files into IGV by clicking ‘Tracks,’ then ‘Local File.’

You can also download IGV locally here

Click here for the TAMA wiki GitHub repository for more information and directions!