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Tutorial RNASeq of comparative transcriptomics based on the species Sparus aurata
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Courses
Tutorial RNASeq differential expression
Transcriptome Assembly
CONTENTS
1. PRELIMINARY INFORMATION
1.1 - Tutorial objective
1.2 - Tutorial material and case study
1.3 - Experiment design and support
1.4 - Installing and activating RNASeq and the Server-Side
2. STEP-BY-STEP MODE TUTORIAL
2.1. - TOPHAT/HISAT2 & CUFFLINKS
2.1.1 - Preparing your experiment
2.1.2 - Quality analysis and preprocessing
2.1.3 - Mapping
2.1.4 - Transcriptome Assembly
2.1.5 - Differential Expression analysis
2.1.6 - GOSeq
2.2. - MAPPING & COUNTING PROTOCOL
2.2.1 - Preparing your experiment
2.2.2 - Quality analysis and preprocessing
2.2.3 - Mapping
2.2.4 - Postprocessing
2.2.5 - Differential Expression analysis
3. PIPELINE MODE TUTORIAL
3.1 - TopHat/Hisat2 & Cufflinks protocol
3.2 - Mapping & Counting protocol
4. BIBLIOGRAPHY
CITE US
Transcriptome Assembly
Cufflinks
ZFG-17-12_03_26333_S7_R1_001
ZFG-17-12_03_26333_S7_R1_001_genes.fpkm_tracking
ZFG-17-12_03_26333_S7_R1_001_isoforms.fpkm_tracking
ZFG-17-12_03_26333_S7_R1_001_skipped.gtf
ZFG-17-12_03_26333_S7_R1_001_transcripts.fasta
ZFG-17-12_03_26333_S7_R1_001_transcripts.gtf
ZFG-17-12_06_26336_S10_R1_001
ZFG-17-12_06_26336_S10_R1_001_genes.fpkm_tracking
ZFG-17-12_06_26336_S10_R1_001_isoforms.fpkm_tracking
ZFG-17-12_06_26336_S10_R1_001_skipped.gtf
ZFG-17-12_06_26336_S10_R1_001_transcripts.fasta
ZFG-17-12_06_26336_S10_R1_001_transcripts.gtf
ZFG-17-12_09_26339_S13_R1_001
ZFG-17-12_09_26339_S13_R1_001_genes.fpkm_tracking
ZFG-17-12_09_26339_S13_R1_001_isoforms.fpkm_tracking
ZFG-17-12_09_26339_S13_R1_001_skipped.gtf
ZFG-17-12_09_26339_S13_R1_001_transcripts.fasta
ZFG-17-12_09_26339_S13_R1_001_transcripts.gtf
ZFG-17-12_12_26342_S16_R1_001
ZFG-17-12_12_26342_S16_R1_001_genes.fpkm_tracking
ZFG-17-12_12_26342_S16_R1_001_isoforms.fpkm_tracking
ZFG-17-12_12_26342_S16_R1_001_skipped.gtf
ZFG-17-12_12_26342_S16_R1_001_transcripts.fasta
ZFG-17-12_12_26342_S16_R1_001_transcripts.gtf
ZFG-17-12_16_26346_S2_R1_001
ZFG-17-12_16_26346_S2_R1_001_genes.fpkm_tracking
ZFG-17-12_16_26346_S2_R1_001_isoforms.fpkm_tracking
ZFG-17-12_16_26346_S2_R1_001_skipped.gtf
ZFG-17-12_16_26346_S2_R1_001_transcripts.fasta
ZFG-17-12_16_26346_S2_R1_001_transcripts.gtf
ZFG-17-12_20_26350_S6_R1_001
ZFG-17-12_20_26350_S6_R1_001_genes.fpkm_tracking
ZFG-17-12_20_26350_S6_R1_001_isoforms.fpkm_tracking
ZFG-17-12_20_26350_S6_R1_001_skipped.gtf
ZFG-17-12_20_26350_S6_R1_001_transcripts.fasta
ZFG-17-12_20_26350_S6_R1_001_transcripts.gtf
ZFG-17-12_24_26354_S10_R1_001
ZFG-17-12_24_26354_S10_R1_001_genes.fpkm_tracking
ZFG-17-12_24_26354_S10_R1_001_isoforms.fpkm_tracking
ZFG-17-12_24_26354_S10_R1_001_skipped.gtf
ZFG-17-12_24_26354_S10_R1_001_transcripts.fasta
ZFG-17-12_24_26354_S10_R1_001_transcripts.gtf
ZFG-17-12_28_26358_S14_R1_001
ZFG-17-12_28_26358_S14_R1_001_genes.fpkm_tracking
ZFG-17-12_28_26358_S14_R1_001_isoforms.fpkm_tracking
ZFG-17-12_28_26358_S14_R1_001_skipped.gtf
ZFG-17-12_28_26358_S14_R1_001_transcripts.fasta
ZFG-17-12_28_26358_S14_R1_001_transcripts.gtf
ZFG-17-12_32_26362_S18_R1_001
ZFG-17-12_32_26362_S18_R1_001_genes.fpkm_tracking
ZFG-17-12_32_26362_S18_R1_001_isoforms.fpkm_tracking
ZFG-17-12_32_26362_S18_R1_001_skipped.gtf
ZFG-17-12_32_26362_S18_R1_001_transcripts.fasta
ZFG-17-12_32_26362_S18_R1_001_transcripts.gtf
Download folder
Transcriptome Assembly
Home
Calendar
Course sections
CONTENTS
1. PRELIMINARY INFORMATION
1.1 - Tutorial objective
1.2 - Tutorial material and case study
1.3 - Experiment design and support
1.4 - Installing and activating RNASeq and the Server-Side
2. STEP-BY-STEP MODE TUTORIAL
2.1. - TOPHAT/HISAT2 & CUFFLINKS
2.1.1 - Preparing your experiment
2.1.2 - Quality analysis and preprocessing
2.1.3 - Mapping
2.1.4 - Transcriptome Assembly
2.1.5 - Differential Expression analysis
2.1.6 - GOSeq
2.2. - MAPPING & COUNTING PROTOCOL
2.2.1 - Prepare your experiment for the mapping & counting analysis
2.2.2 - Quality analysis and preprocessing
2.2.3 - Mapping
2.2.4 - Postprocessing
2.2.5 - Differential Expression analysis
3. PIPELINE MODE TUTORIAL
3.1 - TopHat/Hisat2 & Cufflinks protocol
3.2 - Mapping & Counting protocol
4. BIBLIOGRAPHY
Pipeline mode: Tophat & Cufflinks protocol results
Pipeline mode: Mapping & Counting protocol results
CITE US
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