GTN Proteogenomics1 Database Creation 12
Visit source
Download RO-Crate
Workflow Type: Galaxy
Open
Galaxy workflow
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| FASTQ_ProB_22LIST.fastqsanger | #main/FASTQ_ProB_22LIST.fastqsanger | n/a |
|
| Mus_musculus.GRCm38.86.gtf | #main/Mus_musculus.GRCm38.86.gtf | n/a |
|
| Trimmed_ref_5000_uniprot_cRAP.fasta | #main/Trimmed_ref_5000_uniprot_cRAP.fasta | n/a |
|
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 |
|
| Reference_Protein_Accessions | #main/Reference_Protein_Accessions | n/a |
|
| Uniprot_cRAP_SAV_indel_translatedbed_FASTA | #main/Uniprot_cRAP_SAV_indel_translatedbed_FASTA | n/a |
|
| _anonymous_output_10 | #main/_anonymous_output_10 | n/a |
|
| _anonymous_output_11 | #main/_anonymous_output_11 | n/a |
|
| _anonymous_output_12 | #main/_anonymous_output_12 | n/a |
|
| _anonymous_output_13 | #main/_anonymous_output_13 | n/a |
|
| _anonymous_output_14 | #main/_anonymous_output_14 | n/a |
|
| _anonymous_output_15 | #main/_anonymous_output_15 | n/a |
|
| _anonymous_output_16 | #main/_anonymous_output_16 | n/a |
|
| _anonymous_output_17 | #main/_anonymous_output_17 | n/a |
|
| _anonymous_output_18 | #main/_anonymous_output_18 | n/a |
|
| _anonymous_output_19 | #main/_anonymous_output_19 | n/a |
|
| _anonymous_output_20 | #main/_anonymous_output_20 | n/a |
|
| _anonymous_output_21 | #main/_anonymous_output_21 | n/a |
|
| _anonymous_output_22 | #main/_anonymous_output_22 | n/a |
|
| _anonymous_output_23 | #main/_anonymous_output_23 | n/a |
|
| _anonymous_output_24 | #main/_anonymous_output_24 | n/a |
|
| _anonymous_output_25 | #main/_anonymous_output_25 | n/a |
|
| _anonymous_output_26 | #main/_anonymous_output_26 | n/a |
|
| _anonymous_output_27 | #main/_anonymous_output_27 | n/a |
|
| _anonymous_output_28 | #main/_anonymous_output_28 | n/a |
|
| _anonymous_output_29 | #main/_anonymous_output_29 | n/a |
|
| _anonymous_output_30 | #main/_anonymous_output_30 | n/a |
|
| _anonymous_output_31 | #main/_anonymous_output_31 | n/a |
|
| _anonymous_output_32 | #main/_anonymous_output_32 | n/a |
|
| _anonymous_output_33 | #main/_anonymous_output_33 | n/a |
|
| _anonymous_output_34 | #main/_anonymous_output_34 | 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 |
|
| _anonymous_output_8 | #main/_anonymous_output_8 | n/a |
|
| _anonymous_output_9 | #main/_anonymous_output_9 | n/a |
|
| chr_corrected_gtf | #main/chr_corrected_gtf | n/a |
|
| genomic_mapping_sqlite | #main/genomic_mapping_sqlite | n/a |
|
| variant_annoation_sqlite | #main/variant_annoation_sqlite | n/a |
|
Version History
12 (earliest) Created 22nd Apr 2024 at 11:24 by Helena Rasche
Added/updated 3 files
Open
mastera00d162
Creators and Submitter
Activity
Views: 588 Downloads: 110
Created: 22nd Apr 2024 at 11:24
Last updated: 22nd Apr 2024 at 11:24
Tags AttributionsNone
Related items
https://orcid.org/0000-0001-9760-8992
Advanced Spaces list for this Workflow with search and filtering
No description specified
Teams: Testing, Finn's test team, PNDB, LifeMonitorDev, iPC: individualizedPaediatricCure, test, Test Team, Australian BioCommons Dev, opscientia, V-pipe, UX study leave, DALiuGE workflows, Team1, UX study, My Fancy Team, Team UX Study11, My team, ux study team, UX study koehorst, Team Koehorst, UX Study (satra), Steve's UX Study Test Team, TestSaandra, KJ-workflow-test, NewTeam, team, UXStudy, A Team, UX study K, UXStudy99, Study team, Another new team, UX study2, Team 20220225, my new team, UX Study AU, Testing_proteomics, A test space (KKH), Pleiade, QSM4SENIOR, IGG-Bioinfo, Defragmentation training school, FWCC-D@HZDR, Submission Tutorial, Testing team, Galaxy Training Network, Exploring SEEK SOP functionality, MyTest, Tsinghua University BCI group, Test Team Number Nine, Eli's test team, EMBL Bioimage analysis service, Hu's Test
Web page: Not specified
Advanced Teams list for this Workflow with search and filtering
No description specified
Space: General
Public web page: https://galaxy.training
