GTN Proteogemics2 Database Search
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Download RO-CrateProteogenomics 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 |
|
| Reference Protein Accessions | #main/Reference Protein Accessions | n/a |
|
| 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 |
|
| Peptides_for_BlastP_analysis | #main/Peptides_for_BlastP_analysis | n/a |
|
| Removing reference proteins | #main/Removing reference proteins | n/a |
|
| Search GUI on input dataset(s) | #main/Search GUI on input dataset(s) | n/a |
|
| Selecting sequence with length >6 and <30 | #main/Selecting sequence with length >6 and <30 | n/a |
|
| _anonymous_output_4 | #main/_anonymous_output_4 | n/a |
|
| _anonymous_output_5 | #main/_anonymous_output_5 | n/a |
|
| _anonymous_output_6 | #main/_anonymous_output_6 | n/a |
|
| _anonymous_output_7 | #main/_anonymous_output_7 | n/a |
|
| mz to sqlite on input dataset(s) | #main/mz to sqlite on input dataset(s) | n/a |
|
Version History
7.0 (latest) Created 16th Jul 2024 at 14:07 by Helena Rasche
Added/updated 4 files
Open
master7b98183
8.0 (earliest) Created 25th Jun 2024 at 11:03 by Helena Rasche
Added/updated 4 files
Frozen
8.0c30eee4
Creators and Submitter
Views: 603 Downloads: 186
Created: 25th Jun 2024 at 11:03
Last updated: 25th Jun 2024 at 11:03
Tags AttributionsNone
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