GTN Proteogenomics1 Database Creation

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Workflow Type: Galaxy

Proteogenomics Galaxy Training Network Database Creation

Associated Tutorial

This workflows is part of the tutorial GTN Proteogenomics1 Database Creation, available in the GTN

Thanks to...

Tutorial Author(s): Subina Mehta, Timothy J. Griffin, Pratik Jagtap, Ray Sajulga, James Johnson, Praveen Kumar

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1201?version=2

Inputs

ID Name Description Type
FASTQ_ProB_22LIST.fastqsanger #main/FASTQ_ProB_22LIST.fastqsanger n/a
  • File
Mus_musculus.GRCm38.86.gtf #main/Mus_musculus.GRCm38.86.gtf n/a
  • File
Trimmed_ref_5000_uniprot_cRAP.fasta #main/Trimmed_ref_5000_uniprot_cRAP.fasta n/a
  • File

Steps

ID Name Description
3 HISAT2 toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy5
4 Editing GTF File toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3
5 FASTA-to-Tabular toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1
6 FreeBayes toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1
7 StringTie toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1
8 Filter Tabular toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0
9 CustomProDB toolshed.g2.bx.psu.edu/repos/galaxyp/custom_pro_db/custom_pro_db/1.22.0
10 GffCompare toolshed.g2.bx.psu.edu/repos/iuc/gffcompare/gffcompare/0.11.2
11 SQLite to tabular toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0
12 SQLite to tabular toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0
13 FASTA Merge Files and Filter Unique Sequences toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0
14 FASTA-to-Tabular toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1
15 Convert gffCompare annotated GTF to BED toolshed.g2.bx.psu.edu/repos/galaxyp/gffcompare_to_bed/gffcompare_to_bed/0.2.1
16 Column Regex Find And Replace toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.0
17 Column Regex Find And Replace toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.0
18 FASTA-to-Tabular toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1
19 Filter Tabular toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0
20 Translate BED transcripts toolshed.g2.bx.psu.edu/repos/galaxyp/translate_bed/translate_bed/0.1.0
21 Query Tabular toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0
22 Column Regex Find And Replace toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.0
23 Reference Protein Accessions toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0
24 bed to protein map toolshed.g2.bx.psu.edu/repos/galaxyp/bed_to_protein_map/bed_to_protein_map/0.2.0
25 Tabular-to-FASTA toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1
26 Concatenate datasets toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0
27 FASTA Merge Files and Filter Unique Sequences toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0
28 Genomic_mapping_sqlite toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0

Outputs

ID Name Description Type
CustomProDB_FASTA #main/CustomProDB_FASTA n/a
  • File
Reference_Protein_Accessions #main/Reference_Protein_Accessions n/a
  • File
Uniprot_cRAP_SAV_indel_translatedbed_FASTA #main/Uniprot_cRAP_SAV_indel_translatedbed_FASTA n/a
  • File
_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_4 #main/_anonymous_output_4 n/a
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_anonymous_output_5 #main/_anonymous_output_5 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
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chr_corrected_gtf #main/chr_corrected_gtf n/a
  • File
genomic_mapping_sqlite #main/genomic_mapping_sqlite n/a
  • File
variant_annoation_sqlite #main/variant_annoation_sqlite n/a
  • File

Version History

8.0 (latest) Created 16th Jul 2024 at 14:07 by Helena Rasche

Added/updated 4 files


Open master 339d7de

12.0 (earliest) Created 25th Jun 2024 at 11:09 by Helena Rasche

Added/updated 4 files


Frozen 12.0 e5eda2d
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
GTN Matrix
Tools
HISAT2
FreeBayes
StringTie
customProDB
gffcompare
Biopython
bed to protein map
License
Creative Commons Attribution 4.0 International (CC-BY-4.0)
Activity

Views: 1324   Downloads: 519   Runs: 0

Created: 25th Jun 2024 at 11:09

Last updated: 25th Jun 2024 at 11:09

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