Presentation is loading. Please wait.

Presentation is loading. Please wait.

Do You Want to Build a Transcriptome?

Published byLuiz Gustavo Castilhos Vilarinho Modified over 6 years ago

Similar presentations

Presentation on theme: "Do You Want to Build a Transcriptome?"— Presentation transcript:

1 Do You Want to Build a Transcriptome?

2 Transcriptome Assembly
What tissue(s) How many individuals How many reads and how long Error correct or not Which Assembler? Short reads/long reads Reference guided versus de novo How to evaluate??

3 Transcriptome Assembly
Why easier than genome assembly?

4 Transcriptome Assembly
Why harder than genome assembly?

5 Transcriptome Assembly
What tissues?

6 Transcriptome Assembly
How Many Individuals??

7 Transcriptome Assembly
How Many Reads??

8 Transcriptome Assembly
How Many Reads??

9 Transcriptome Assembly

10 Transcriptome Assembly
Error Correct??

11 Transcriptome Assembly
Which Assembler??

12 Transcriptome Assembly
How To Evaluate TransRate BUSCO Mapping reads Mapping transcripts

13 Transcriptome Assembly
Short reads/long reads Reference guided versus de novo

Download ppt "Do You Want to Build a Transcriptome?"

Similar presentations

What is neural stemness? Why is it important? What are the molecular signatures of neural stemness? What are the regulatory networks that control neural.

What is neural stemness? Why is it important? What are the molecular signatures of neural stemness? What are the regulatory networks that control neural.
Capturing the chicken transcriptome with PacBio long read RNA-seq data OR Chicken in awesome sauce: a recipe for new transcript identification Gladstone.

Capturing the chicken transcriptome with PacBio long read RNA-seq data OR Chicken in awesome sauce: a recipe for new transcript identification Gladstone.
MCB3895-004 Lecture #15 Oct 23/14 De novo assemblies using PacBio.

MCB Lecture #15 Oct 23/14 De novo assemblies using PacBio.
1/03/09 De 89 à 98. 1/03/09 De 89 à 98 1/03/09 De 89 à 98.

1/03/09 De 89 à 98. 1/03/09 De 89 à 98 1/03/09 De 89 à 98.
Transcriptome Sequencing with Reference

Transcriptome Sequencing with Reference
Peter Tsai Bioinformatics Institute, University of Auckland

Peter Tsai Bioinformatics Institute, University of Auckland
Xiaole Shirley Liu STAT115, STAT215, BIO298, BIST520

Xiaole Shirley Liu STAT115, STAT215, BIO298, BIST520
Transcriptomics Jim Noonan GENE 760.

Transcriptomics Jim Noonan GENE 760.
Objective Exam Score Distribution. Item 12345678910 Difficulty 0.420.950.820.660.890.870.760.340.680.92 Power 0.630.110.160.470.110.260.16 0.210.05 Item11121314151617181920.

Objective Exam Score Distribution. Item Difficulty Power Item
NGS Transcriptomic Workflows Hugh Shanahan & Jamie al-Nasir Royal Holloway, University of London.

NGS Transcriptomic Workflows Hugh Shanahan & Jamie al-Nasir Royal Holloway, University of London.
I. defining genomes and their contents 2002: Sanger sequencing technology (few, long reads) EST projects (random cDNA clones) cloned gDNA (cosmids, fosmids,

I. defining genomes and their contents 2002: Sanger sequencing technology (few, long reads) EST projects (random cDNA clones) cloned gDNA (cosmids, fosmids,
Titus Brown Qingpeng Zhang John Blischak Welcome!.

Titus Brown Qingpeng Zhang John Blischak Welcome!.
Next generation sequencing Xusheng Wang 4/29/2010.

Next generation sequencing Xusheng Wang 4/29/2010.
De-novo Assembly Day 4.

De-novo Assembly Day 4.
CS 394C March 19, 2012 Tandy Warnow.

CS 394C March 19, 2012 Tandy Warnow.
Todd J. Treangen, Steven L. Salzberg

Todd J. Treangen, Steven L. Salzberg
PE-Assembler: De novo assembler using short paired-end reads Pramila Nuwantha Ariyaratne.

PE-Assembler: De novo assembler using short paired-end reads Pramila Nuwantha Ariyaratne.
How I learned to quit worrying Deanna M. Church Staff Scientist, Short Course in Medical Genetics 2013 And love multiple coordinate.

How I learned to quit worrying Deanna M. Church Staff Scientist, Short Course in Medical Genetics 2013 And love multiple coordinate.
June 11, 2013 Intro to Bioinformatics – Assembling a Transcriptome Tom Doak Carrie Ganote National Center for Genome Analysis Support.

June 11, 2013 Intro to Bioinformatics – Assembling a Transcriptome Tom Doak Carrie Ganote National Center for Genome Analysis Support.
Next Generation Sequencing and its data analysis challenges Background Alignment and Assembly Applications Genome Epigenome Transcriptome.

Next Generation Sequencing and its data analysis challenges Background Alignment and Assembly Applications Genome Epigenome Transcriptome.

Similar presentations

Ads by Google