De novo transcriptome reconstruction with RNA-Seq
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Workflow Type: Galaxy

De novo transcriptome reconstruction with RNA-Seq

Associated Tutorial

This workflows is part of the tutorial De novo transcriptome reconstruction with RNA-Seq, available in the GTN

Thanks to...

Tutorial Author(s): Mallory Freeberg, Mo Heydarian

Tutorial Contributor(s): James Taylor

SEEK ID: https://dev.workflowhub.eu/workflows/1319?version=1

Inputs

ID	Name	Description	Type
G1E_rep1_forward_read	#main/G1E_rep1_forward_read	n/a	File
G1E_rep1_reverse_read	#main/G1E_rep1_reverse_read	n/a	File
G1E_rep2_forward_read	#main/G1E_rep2_forward_read	n/a	File
G1E_rep2_reverse_read	#main/G1E_rep2_reverse_read	n/a	File
Megakaryocyte_rep1_forward_read	#main/Megakaryocyte_rep1_forward_read	n/a	File
Megakaryocyte_rep1_reverse_read	#main/Megakaryocyte_rep1_reverse_read	n/a	File
Megakaryocyte_rep2_forward_read	#main/Megakaryocyte_rep2_forward_read	n/a	File
Megakaryocyte_rep2_reverse_read	#main/Megakaryocyte_rep2_reverse_read	n/a	File
RefSeq_reference_GTF	#main/RefSeq_reference_GTF	n/a	File

Steps

ID	Name	Description
9	FastQC	toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
10	FastQC	toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
11	Trimmomatic	toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0
12	FastQC	toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
13	FastQC	toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
14	Trimmomatic	toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0
15	FastQC	toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
16	FastQC	toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
17	Trimmomatic	toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0
18	FastQC	toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
19	FastQC	toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
20	Trimmomatic	toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.38.0
21	HISAT2	toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy5
22	FastQC	toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
23	FastQC	toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
24	HISAT2	toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy5
25	FastQC	toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
26	FastQC	toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
27	HISAT2	toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy5
28	FastQC	toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
29	FastQC	toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
30	HISAT2	toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy5
31	FastQC	toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
32	FastQC	toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
33	StringTie	toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.3.6
34	bamCoverage	toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.0.0.0
35	bamCoverage	toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.0.0.0
36	StringTie	toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.3.6
37	bamCoverage	toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.0.0.0
38	bamCoverage	toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.0.0.0
39	StringTie	toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.3.6
40	bamCoverage	toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.0.0.0
41	bamCoverage	toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.0.0.0
42	StringTie	toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.3.6
43	bamCoverage	toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.0.0.0
44	bamCoverage	toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.0.0.0
45	StringTie merge	toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/1.3.6
46	GffCompare	toolshed.g2.bx.psu.edu/repos/iuc/gffcompare/gffcompare/0.11.2
47	featureCounts	toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.4+galaxy1
48	featureCounts	toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.4+galaxy1
49	featureCounts	toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.4+galaxy1
50	featureCounts	toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.4+galaxy1
51	DESeq2	toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6
52	Filter	Filter1
53	Filter	Filter1
54	Filter	Filter1

Outputs

ID	Name	Description	Type
_anonymous_output_10	#main/_anonymous_output_10	n/a	File
_anonymous_output_11	#main/_anonymous_output_11	n/a	File
_anonymous_output_12	#main/_anonymous_output_12	n/a	File
_anonymous_output_13	#main/_anonymous_output_13	n/a	File
_anonymous_output_14	#main/_anonymous_output_14	n/a	File
_anonymous_output_15	#main/_anonymous_output_15	n/a	File
_anonymous_output_16	#main/_anonymous_output_16	n/a	File
_anonymous_output_17	#main/_anonymous_output_17	n/a	File
_anonymous_output_18	#main/_anonymous_output_18	n/a	File
_anonymous_output_19	#main/_anonymous_output_19	n/a	File
_anonymous_output_20	#main/_anonymous_output_20	n/a	File
_anonymous_output_21	#main/_anonymous_output_21	n/a	File
_anonymous_output_22	#main/_anonymous_output_22	n/a	File
_anonymous_output_23	#main/_anonymous_output_23	n/a	File
_anonymous_output_24	#main/_anonymous_output_24	n/a	File
_anonymous_output_25	#main/_anonymous_output_25	n/a	File
_anonymous_output_26	#main/_anonymous_output_26	n/a	File
_anonymous_output_27	#main/_anonymous_output_27	n/a	File
_anonymous_output_28	#main/_anonymous_output_28	n/a	File
_anonymous_output_29	#main/_anonymous_output_29	n/a	File
_anonymous_output_30	#main/_anonymous_output_30	n/a	File
_anonymous_output_31	#main/_anonymous_output_31	n/a	File
_anonymous_output_32	#main/_anonymous_output_32	n/a	File
_anonymous_output_33	#main/_anonymous_output_33	n/a	File
_anonymous_output_34	#main/_anonymous_output_34	n/a	File
_anonymous_output_35	#main/_anonymous_output_35	n/a	File
_anonymous_output_36	#main/_anonymous_output_36	n/a	File
_anonymous_output_37	#main/_anonymous_output_37	n/a	File
_anonymous_output_38	#main/_anonymous_output_38	n/a	File
_anonymous_output_39	#main/_anonymous_output_39	n/a	File
_anonymous_output_40	#main/_anonymous_output_40	n/a	File
_anonymous_output_41	#main/_anonymous_output_41	n/a	File
_anonymous_output_42	#main/_anonymous_output_42	n/a	File
_anonymous_output_43	#main/_anonymous_output_43	n/a	File
_anonymous_output_44	#main/_anonymous_output_44	n/a	File
_anonymous_output_45	#main/_anonymous_output_45	n/a	File
_anonymous_output_46	#main/_anonymous_output_46	n/a	File
_anonymous_output_47	#main/_anonymous_output_47	n/a	File
_anonymous_output_48	#main/_anonymous_output_48	n/a	File
_anonymous_output_49	#main/_anonymous_output_49	n/a	File
_anonymous_output_50	#main/_anonymous_output_50	n/a	File