NGS : RNA-seq differential expression analysis

Created: 2014-02-27 17:40:37 Last updated: 2014-06-10 09:18:53

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Analyse paired-end RNA-seq reads of 2 different individuals with FastQC, Tophat2, Cufflinks and Cuffdiff using a reference annotation in gtf format

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Inputs (7)

Name	Description
Fastq Forward reads
Fastq Reverse reads
refGenomeSource	runtime parameter for tool Tophat2
Fastq Forward reads
Fastq Reverse reads
Input Dataset
refGenomeSource	runtime parameter for tool Tophat2

Steps (17)

Name	Tool	Description
Input dataset	None
Input dataset	None
Tophat2	tophat2
Cufflinks	toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/0.0.6
Merge BAM Files	toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.1.2
Cufflinks	toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/0.0.6
Cufflinks	toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/0.0.6
Cuffdiff	toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/cuffdiff/0.0.6
Filter	testtoolshed.g2.bx.psu.edu/repos/greg/gregs_filter/Filter1/3.3.0
Input dataset	None
Input dataset	None
Input dataset	None
FastQC:Read QC	fastqc
FastQC:Read QC	fastqc
Tophat2	tophat2
FastQC:Read QC	fastqc
FastQC:Read QC	fastqc

Outputs (46)

Name	Type
align_summary	txt
fusions	tabular
insertions	bed
deletions	bed
junctions	bed
accepted_hits	bam
genes_expression	tabular
transcripts_expression	tabular
assembled_isoforms	gtf
total_map_mass	txt
output1	bam
outlog	txt
genes_expression	tabular
transcripts_expression	tabular
assembled_isoforms	gtf
total_map_mass	txt
genes_expression	tabular
transcripts_expression	tabular
assembled_isoforms	gtf
total_map_mass	txt
isoforms_read_group	tabular
genes_read_group	tabular
cds_read_group	tabular
tss_groups_read_group	tabular
splicing_diff	tabular
promoters_diff	tabular
cds_diff	tabular
cds_exp_fpkm_tracking	tabular
cds_fpkm_tracking	tabular
tss_groups_exp	tabular
tss_groups_fpkm_tracking	tabular
genes_exp	tabular
genes_fpkm_tracking	tabular
isoforms_exp	tabular
isoforms_fpkm_tracking	tabular
out_file1	input
html_file	html
html_file	html
align_summary	txt
fusions	tabular
insertions	bed
deletions	bed
junctions	bed
accepted_hits	bam
html_file	html
html_file	html

Information Workflow Type

Galaxy

Information Uploader

Ylebras

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Information Version 1 (of 1)

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Ylebras

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Information Favourited By (1)

Leonardo Terra

Information Statistics

1330 viewings

767 downloads

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Citations (1)

1. Y. Le Bras, A. Roult, C. Monjeaud, M. Bahin, O. Quenez, C. Heriveau, A. Bretaudeau, O. Sallou, O. Collin, Towards a Life Sciences Virtual Research Environment : an e-Science initiative in Western France, JOBIM 2013, 03 July 2013, https://www.e-biogenouest.org/resources/128

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NGS : RNA-seq differential expression analysis

Created by Ylebras on Thursday 27 February 2014 17:40:37 (UTC)

Last edited by Ylebras on Thursday 27 February 2014 17:41:10 (UTC)

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