Essential genes detection with Transposon insertion sequencing
Version 1

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Workflow Type: Galaxy

Galaxy workflow

SEEK ID: https://dev.workflowhub.eu/workflows/887?version=1

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

6 (earliest) Created 22nd Apr 2024 at 10:50 by Helena Rasche

Added/updated 3 files


Open master 2e2761b
help Creators and Submitter
Creators
Not specified
Submitter
Tools
Cutadapt
TRANSIT
Bowtie
DeepTools
License
Creative Commons Attribution 4.0 International
Activity

Views: 45

Created: 22nd Apr 2024 at 10:50

Last updated: 22nd Apr 2024 at 10:50

help Attributions

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Total size: 74.7 KB
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