Essential genes detection with Transposon insertion sequencing

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Workflow Type: Galaxy

Essential genes detection with Transposon insertion sequencing

Associated Tutorial

This workflows is part of the tutorial Essential genes detection with Transposon insertion sequencing, available in the GTN

Features

Thanks to...

Tutorial Author(s): Delphine Lariviere, Bérénice Batut

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1149?version=2

Inputs

ID Name Description Type
Tnseq-Tutorial-reads.fastqsanger.gz #main/Tnseq-Tutorial-reads.fastqsanger.gz n/a
  • File
condition_barcodes.fasta #main/condition_barcodes.fasta n/a
  • File
construct_barcodes.fasta #main/construct_barcodes.fasta n/a
  • File
staph_aur.fasta #main/staph_aur.fasta n/a
  • File
staph_aur.gff3 #main/staph_aur.gff3 n/a
  • File

Steps

ID Name Description
5 Cutadapt toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5
6 Nucleotide subsequence search toolshed.g2.bx.psu.edu/repos/bgruening/find_subsequences/bg_find_subsequences/0.2
7 Convert GFF3 toolshed.g2.bx.psu.edu/repos/iuc/gff_to_prot/gff_to_prot/3.0.2+galaxy0
8 Cutadapt toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5
9 Cut Cut1
10 Cut Cut1
11 Cutadapt toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5
12 Compute toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0
13 Cutadapt toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5
14 Cut Cut1
15 Cutadapt toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5
16 Map with Bowtie for Illumina toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.2.0
17 bamCoverage toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0
18 Join toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2
19 Join toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2
20 Cut Cut1
21 Cut Cut1
22 Sort toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1
23 Compute toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0
24 Cut Cut1
25 Sort toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1
26 Join toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2
27 Compute toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0
28 Cut Cut1
29 Sort toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1
30 Gumbel toolshed.g2.bx.psu.edu/repos/iuc/transit_gumbel/transit_gumbel/3.0.2+galaxy0
31 Filter Filter1
32 Extract Dataset __EXTRACT_DATASET__
33 Extract Dataset __EXTRACT_DATASET__
34 Join toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2
35 Join toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2
36 Join toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2

Outputs

ID Name Description Type
_anonymous_output_10 #main/_anonymous_output_10 n/a
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_anonymous_output_11 #main/_anonymous_output_11 n/a
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_anonymous_output_12 #main/_anonymous_output_12 n/a
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_anonymous_output_13 #main/_anonymous_output_13 n/a
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_anonymous_output_14 #main/_anonymous_output_14 n/a
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_anonymous_output_15 #main/_anonymous_output_15 n/a
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_anonymous_output_16 #main/_anonymous_output_16 n/a
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_anonymous_output_17 #main/_anonymous_output_17 n/a
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_anonymous_output_18 #main/_anonymous_output_18 n/a
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_anonymous_output_19 #main/_anonymous_output_19 n/a
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_anonymous_output_20 #main/_anonymous_output_20 n/a
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_anonymous_output_21 #main/_anonymous_output_21 n/a
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_anonymous_output_22 #main/_anonymous_output_22 n/a
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_anonymous_output_23 #main/_anonymous_output_23 n/a
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_anonymous_output_24 #main/_anonymous_output_24 n/a
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_anonymous_output_25 #main/_anonymous_output_25 n/a
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_anonymous_output_26 #main/_anonymous_output_26 n/a
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_anonymous_output_27 #main/_anonymous_output_27 n/a
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_anonymous_output_28 #main/_anonymous_output_28 n/a
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_anonymous_output_29 #main/_anonymous_output_29 n/a
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_anonymous_output_30 #main/_anonymous_output_30 n/a
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_anonymous_output_31 #main/_anonymous_output_31 n/a
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_anonymous_output_32 #main/_anonymous_output_32 n/a
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_anonymous_output_33 #main/_anonymous_output_33 n/a
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_anonymous_output_34 #main/_anonymous_output_34 n/a
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_anonymous_output_35 #main/_anonymous_output_35 n/a
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_anonymous_output_36 #main/_anonymous_output_36 n/a
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_anonymous_output_37 #main/_anonymous_output_37 n/a
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_anonymous_output_6 #main/_anonymous_output_6 n/a
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_anonymous_output_7 #main/_anonymous_output_7 n/a
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_anonymous_output_8 #main/_anonymous_output_8 n/a
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_anonymous_output_9 #main/_anonymous_output_9 n/a
  • File
condition #main/condition n/a
  • File
control #main/control n/a
  • File
essential_both #main/essential_both n/a
  • File
essential_condition #main/essential_condition n/a
  • File
essential_control #main/essential_control n/a
  • File

Version History

1.0 (latest) Created 16th Jul 2024 at 14:05 by Helena Rasche

Added/updated 4 files


Open master 77bfa1d

6.0 (earliest) Created 25th Jun 2024 at 11:03 by Helena Rasche

Added/updated 4 files


Frozen 6.0 088703d
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Activity

Views: 227   Downloads: 91

Created: 25th Jun 2024 at 11:03

Last updated: 25th Jun 2024 at 11:03

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