Training Sanger sequences CHD8
Visit source
Download RO-CrateAssociated Tutorial
This workflows is part of the tutorial Training Sanger sequences CHD8, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): Coline Royaux
Workflow Author(s): Coline Royaux
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| AOPEP_and_CHD8_sequences_20220907.zip?download=1 | AOPEP_and_CHD8_sequences_20220907.zip?download=1 | n/a |
|
| Prim | Prim | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 2 | Unzip | toolshed.g2.bx.psu.edu/repos/imgteam/unzip/unzip/6.0+galaxy0 |
| 3 | Filter FASTA | toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.3 |
| 4 | Filter FASTA | toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.3 |
| 5 | Extract element identifiers | toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2 |
| 6 | Degap.seqs | toolshed.g2.bx.psu.edu/repos/iuc/mothur_degap_seqs/mothur_degap_seqs/1.39.5.0 |
| 7 | Degap.seqs | toolshed.g2.bx.psu.edu/repos/iuc/mothur_degap_seqs/mothur_degap_seqs/1.39.5.0 |
| 8 | Regex Find And Replace | toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3 |
| 9 | Regex Find And Replace | toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3 |
| 10 | Reverse-Complement | toolshed.g2.bx.psu.edu/repos/devteam/fastx_reverse_complement/cshl_fastx_reverse_complement/1.0.2+galaxy0 |
| 11 | Filter collection | __FILTER_FROM_FILE__ |
| 12 | Filter collection | __FILTER_FROM_FILE__ |
| 13 | ab1 to FASTQ converter | toolshed.g2.bx.psu.edu/repos/ecology/ab1_fastq_converter/ab1_fastq_converter/1.20.0 |
| 14 | ab1 to FASTQ converter | toolshed.g2.bx.psu.edu/repos/ecology/ab1_fastq_converter/ab1_fastq_converter/1.20.0 |
| 15 | seqtk_trimfq | toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_trimfq/1.3.1 |
| 16 | seqtk_trimfq | toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_trimfq/1.3.1 |
| 17 | FASTQ Groomer | toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 |
| 18 | Sort collection | __SORTLIST__ |
| 19 | Sort collection | __SORTLIST__ |
| 20 | Reverse-Complement | toolshed.g2.bx.psu.edu/repos/devteam/fastx_reverse_complement/cshl_fastx_reverse_complement/1.0.2+galaxy0 |
| 21 | seqtk_mergepe | toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_mergepe/1.3.1 |
| 22 | FASTQ Groomer | toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 |
| 23 | FASTQ to Tabular | toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_tabular/fastq_to_tabular/1.1.5 |
| 24 | Tabular-to-FASTA | toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1 |
| 25 | Align sequences | toolshed.g2.bx.psu.edu/repos/iuc/qiime_align_seqs/qiime_align_seqs/1.9.1.0 |
| 26 | Consensus sequence from aligned FASTA | toolshed.g2.bx.psu.edu/repos/ecology/aligned_to_consensus/aligned_to_consensus/1.0.0 |
| 27 | Merge.files | toolshed.g2.bx.psu.edu/repos/iuc/mothur_merge_files/mothur_merge_files/1.39.5.0 |
| 28 | Merge.files | toolshed.g2.bx.psu.edu/repos/iuc/mothur_merge_files/mothur_merge_files/1.39.5.0 |
| 29 | Regex Find And Replace | toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3 |
| 30 | Align sequences | toolshed.g2.bx.psu.edu/repos/iuc/qiime_align_seqs/qiime_align_seqs/1.9.1.0 |
| 31 | NCBI BLAST+ blastn | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.10.1+galaxy2 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| _anonymous_output_1 | _anonymous_output_1 | n/a |
|
Version History
1.0 (latest) Created 16th Jul 2024 at 14:24 by Helena Rasche
Added/updated 4 files
Open
masterb87672a
2.0 (earliest) Created 25th Jun 2024 at 11:20 by Helena Rasche
Added/updated 4 files
Frozen
2.0fe32af9
Creators and Submitter
Views: 427 Downloads: 135
Created: 25th Jun 2024 at 11:20
Last updated: 25th Jun 2024 at 11:20
AttributionsNone
Related items
https://orcid.org/0000-0001-9760-8992
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
Space: General
Public web page: https://galaxy.training
