Practical Bioinformatics Mark Voorhies 5/29/2019 Mark Voorhies - - PowerPoint PPT Presentation

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Nov 15, 2022 343 likes •521 views

Practical Bioinformatics Mark Voorhies 5/29/2019 Mark Voorhies Practical Bioinformatics Example Pipeline: Overview Mark Voorhies Practical Bioinformatics Example Pipeline: Overview Generate Genome Transfer Pre-process Samples Coverage

SLIDE 1

Practical Bioinformatics

Mark Voorhies 5/29/2019

Mark Voorhies Practical Bioinformatics

SLIDE 2

Example Pipeline: Overview

Mark Voorhies Practical Bioinformatics

SLIDE 3

Example Pipeline: Overview

Generate Samples Transfer & Archival Pre-process Genome Coverage Transcriptome Profile Differential Expression Annotation/ Analysis Paper

~2.5-4 years (publish)

Mark Voorhies Practical Bioinformatics

SLIDE 4

Example Pipeline: Overview

Generate Samples Transfer & Archival Pre-process Genome Coverage Transcriptome Profile Differential Expression Annotation/ Analysis Paper

~2.5-4 years (publish) ~1 day

Mark Voorhies Practical Bioinformatics

SLIDE 5

Example Pipeline: Overview

Generate Samples Transfer & Archival Pre-process Genome Coverage Transcriptome Profile Differential Expression Annotation/ Analysis Paper

~2.5-4 years (publish) ~1 day Follow-up Experiments

Mark Voorhies Practical Bioinformatics

SLIDE 6

Example Pipeline: Overview

Generate Samples Transfer & Archival Pre-process Genome Coverage Transcriptome Profile Differential Expression Annotation/ Analysis Paper

~2.5-4 years (publish) ~1 day Follow-up Experiments

Mark Voorhies Practical Bioinformatics

SLIDE 7

Example Pipeline: Overview

Mark Voorhies Practical Bioinformatics

SLIDE 8

Example Pipeline: Details

Mark Voorhies Practical Bioinformatics

SLIDE 9

GSE88801 Pipelines

Mark Voorhies Practical Bioinformatics

SLIDE 10

Abundance estimation with kallisto

Index transcript kmers

Mark Voorhies Practical Bioinformatics

SLIDE 11

Abundance estimation with kallisto

Index transcript kmers Assume a uniform transcriptional profile

transcript abundance

Mark Voorhies Practical Bioinformatics

SLIDE 12

Abundance estimation with kallisto

Index transcript kmers Assume a uniform transcriptional profile

transcript abundance

Assign reads based on profile

Mark Voorhies Practical Bioinformatics

SLIDE 13

Abundance estimation with kallisto

Index transcript kmers Assume a uniform transcriptional profile

transcript abundance

Assign reads based on profile Update profile based

n assignments

transcript abundance

Mark Voorhies Practical Bioinformatics

SLIDE 14

Abundance estimation with kallisto

Index transcript kmers Assume a uniform transcriptional profile

transcript abundance

Assign reads based on profile Update profile based

n assignments

transcript abundance

Mark Voorhies Practical Bioinformatics

SLIDE 15

Abundance estimation with kallisto

Index transcript kmers Assume a uniform transcriptional profile

transcript abundance

Assign reads based on profile Update profile based

n assignments

transcript abundance transcript abundance

Mark Voorhies Practical Bioinformatics

SLIDE 16

Abundance estimation with kallisto

export transcriptome=”GRCm38 all mRNA” while read i ; do export jobname=”${ i }. ${ transcriptome }. f r ” k a l l i s t o quant −i ”${ transcriptome }. idx ” \ −t 4 −−s i n g l e −−fr −stranded −l 250 −s 50 −o ”${jobname}” ”${ i } 1 . f a s t q . gz” \ > ”${jobname }. log ” \ 2> ”${jobname }. e r r ” done < sample names . t x t

Mark Voorhies Practical Bioinformatics