De novo transcriptome reconstruction with RNA-Seq
5.0

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, Saskia Hiltemann, Nicola Soranzo, Helena Rasche, Anthony Bretaudeau, Gildas Le Corguillé, Björn Grüning, Mallory Freeberg, Mo Heydarian, Bérénice Batut, William Durand, Niall Beard

gtn star logo followed by the word workflows

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

Version History

5.0 (earliest) Created 2nd Jun 2025 at 11:04 by GTN Bot

Added/updated 4 files


Open master 573a9a1
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
Activity

Views: 54   Downloads: 6   Runs: 0

Created: 2nd Jun 2025 at 11:04

help Attributions

None

Total size: 415 KB
Powered by
(v.1.17.0-main)
Copyright © 2008 - 2025 The University of Manchester and HITS gGmbH