Workflow Type: Galaxy
Associated Tutorial
This workflows is part of the tutorial Proteogenomics 1: Database Creation, available in the GTN
Features
- Includes a Galaxy Workflow Report
Thanks to...
Tutorial Author(s): Subina Mehta, Timothy J. Griffin, Pratik Jagtap, Ray Sajulga, James Johnson, Praveen Kumar
Inputs
ID | Name | Description | Type |
---|---|---|---|
FASTQ_ProB_22LIST.fastqsanger | FASTQ_ProB_22LIST.fastqsanger | n/a |
|
Reference Annotation | Reference Annotation | n/a |
|
Reference Genome | Reference Genome | n/a |
|
Reference Genome Annotation for CustomProDB | Reference Genome Annotation for CustomProDB | n/a |
|
Trimmed_ref_5000_uniprot_cRAP.fasta | Trimmed_ref_5000_uniprot_cRAP.fasta | n/a |
|
Steps
ID | Name | Description |
---|---|---|
5 | Filter Tabular | toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.3.1 |
6 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.5+galaxy0 |
7 | HISAT2 | toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1 |
8 | FreeBayes | toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.9+galaxy0 |
9 | StringTie | toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0 |
10 | CustomProDB | toolshed.g2.bx.psu.edu/repos/galaxyp/custom_pro_db/custom_pro_db/1.22.0 |
11 | GffCompare | toolshed.g2.bx.psu.edu/repos/iuc/gffcompare/gffcompare/0.12.6+galaxy0 |
12 | 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 |
13 | SQLite to tabular | toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/3.2.1 |
14 | SQLite to tabular | toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/3.2.1 |
15 | FASTA-to-Tabular | toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1 |
16 | Convert gffCompare annotated GTF to BED | toolshed.g2.bx.psu.edu/repos/galaxyp/gffcompare_to_bed/gffcompare_to_bed/0.2.1 |
17 | FASTA-to-Tabular | toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1 |
18 | Column Regex Find And Replace | toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3 |
19 | Column Regex Find And Replace | toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3 |
20 | Filter Tabular | toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.3.1 |
21 | Translate BED transcripts | toolshed.g2.bx.psu.edu/repos/galaxyp/translate_bed/translate_bed/0.1.0 |
22 | Column Regex Find And Replace | toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3 |
23 | Query Tabular | toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2 |
24 | Concatenate multiple datasets | toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets/1.4.3 |
25 | bed to protein map | toolshed.g2.bx.psu.edu/repos/galaxyp/bed_to_protein_map/bed_to_protein_map/0.2.0 |
26 | Tabular-to-FASTA | toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1 |
27 | Concatenate multiple datasets | toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets/1.4.3 |
28 | 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 |
29 | Query Tabular | toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
Reference Annotation fixed.gtf | Reference Annotation fixed.gtf | n/a |
|
HISAT_Output.BAM | HISAT_Output.BAM | n/a |
|
Stringtie_output.gtf | Stringtie_output.gtf | n/a |
|
transcripts_annotated | transcripts_annotated | n/a |
|
Merged and Filtered FASTA from CustomProDB | Merged and Filtered FASTA from CustomProDB | n/a |
|
genomic_mapping_sqlite | genomic_mapping_sqlite | n/a |
|
variant_annotation_sqlite | variant_annotation_sqlite | n/a |
|
SAV_INDEL | SAV_INDEL | n/a |
|
variant_annotation | variant_annotation | n/a |
|
Translate cDNA_minus_CDS | Translate cDNA_minus_CDS | n/a |
|
Variant_annotation_sqlitedb | Variant_annotation_sqlitedb | n/a |
|
CustomProDB Merged Fasta | CustomProDB Merged Fasta | n/a |
|
Genomic_Protein_map | Genomic_Protein_map | n/a |
|
Uniprot_cRAP_SAV_indel_translatedbed | Uniprot_cRAP_SAV_indel_translatedbed | n/a |
|
genomic_mapping_sqlitedb | genomic_mapping_sqlitedb | n/a |
|
Version History

Creators
Not specifiedSubmitter
Discussion Channel
Activity
Views: 37 Downloads: 2 Runs: 0
Created: 2nd Jun 2025 at 10:51

None