Workflow Type: Galaxy
Open
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Proteogenomics 2: Database Search
Associated Tutorial
This workflows is part of the tutorial GTN Proteogemics2 Database Search, available in the GTN
Thanks to...
Tutorial Author(s): Subina Mehta, Timothy J. Griffin, Pratik Jagtap, Ray Sajulga, James Johnson, Praveen Kumar
Inputs
ID | Name | Description | Type |
---|---|---|---|
MGF Collection | #main/MGF Collection | n/a |
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Reference Protein Accessions | #main/Reference Protein Accessions | n/a |
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Uniprot_cRAP_SAV_indel_translatedbed.FASTA | #main/Uniprot_cRAP_SAV_indel_translatedbed.FASTA | n/a |
|
Steps
ID | Name | Description |
---|---|---|
3 | Search GUI | toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.10.1 |
4 | Peptide Shaker | toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3 |
5 | mz to sqlite | toolshed.g2.bx.psu.edu/repos/galaxyp/mz_to_sqlite/mz_to_sqlite/2.0.4+galaxy1 |
6 | Removing reference proteins | toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0 |
7 | Selecting sequence with length >6 and <30 | toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0 |
8 | Peptides for BlastP analysis | toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
Peptide Shaker on input dataset(s): mzidentML file | #main/Peptide Shaker on input dataset(s): mzidentML file | n/a |
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Peptides_for_BlastP_analysis | #main/Peptides_for_BlastP_analysis | n/a |
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Removing reference proteins | #main/Removing reference proteins | n/a |
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Search GUI on input dataset(s) | #main/Search GUI on input dataset(s) | n/a |
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Selecting sequence with length >6 and <30 | #main/Selecting sequence with length >6 and <30 | 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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mz to sqlite on input dataset(s) | #main/mz to sqlite on input dataset(s) | n/a |
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Version History
7.0 (latest) Created 16th Jul 2024 at 14:07 by Helena Rasche
Added/updated 4 files
Open
master
7b98183
8.0 (earliest) Created 25th Jun 2024 at 11:03 by Helena Rasche
Added/updated 4 files
Frozen
8.0
c30eee4
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Views: 189 Downloads: 80
Created: 25th Jun 2024 at 11:03
Last updated: 25th Jun 2024 at 11:03
![help](/assets/famfamfam_silk/information-8cfe563be76fb11b27c8ba778f5d40ce6800b244d6ca58ef6e9973308efbe534.png)
![help](/assets/famfamfam_silk/information-8cfe563be76fb11b27c8ba778f5d40ce6800b244d6ca58ef6e9973308efbe534.png)
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