Genome-wide alternative splicing analysis: human Version 1
Visit source
Download RO Crate
Workflow Type: Galaxy
Open
Galaxy workflow
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Active sites dataset | Active sites dataset | Active sites dataset. |
|
| CPAT header | CPAT header | Galaxy compatible CPAT header. |
|
| Control IDs | Control IDs | IDs of control sequences, corresponding to filenames. |
|
| Factor 01 | Factor 01 | First factor name. |
|
| Factor 02 | Factor 02 | Second factor name. |
|
| Genome annotation | Genome annotation | Reference genome annotation in GTF format. |
|
| Pfam-A HMM Stockholm file | Pfam-A HMM Stockholm file | Stockholm file. |
|
| Pfam-A HMM library | Pfam-A HMM library | HMM library. |
|
| RNA-seq data collection | RNA-seq data collection | Collection of paired-end RNA-seq datasets. |
|
| Reference genome | Reference genome | Genome reference in FASTA format. |
|
Steps
| ID | Name | Description |
|---|---|---|
| 10 | fastp | toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0 |
| 11 | Flatten collection | __FLATTEN__ |
| 12 | Search in textfiles | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1 |
| 13 | Search in textfiles | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1 |
| 14 | Convert GTF to BED12 | toolshed.g2.bx.psu.edu/repos/iuc/gtftobed12/gtftobed12/357 |
| 15 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0 |
| 16 | gffread | toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.3+galaxy0 |
| 17 | gffread | toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.3+galaxy0 |
| 18 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1 |
| 19 | Search in textfiles | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1 |
| 20 | Concatenate datasets | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1 |
| 21 | Search in textfiles | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1 |
| 22 | Cut | Cut1 |
| 23 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2 |
| 24 | Parse parameter value | param_value_from_file |
| 25 | RNA STAR | toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy3 |
| 26 | Concatenate datasets | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1 |
| 27 | Text reformatting | ($5 > 0 && $7 > 3 && $6==0) toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2 |
| 28 | Cut | Cut1 |
| 29 | Sort | sort1 |
| 30 | Unique | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0 |
| 31 | RNA STAR | toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy3 |
| 32 | StringTie | toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.1+galaxy1 |
| 33 | Junction Annotation | toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_annotation/5.0.1+galaxy2 |
| 34 | Junction Saturation | toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_saturation/5.0.1+galaxy2 |
| 35 | Gene Body Coverage (BAM) | toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/5.0.1+galaxy2 |
| 36 | Inner Distance | toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_inner_distance/5.0.1+galaxy2 |
| 37 | Infer Experiment | toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/5.0.1+galaxy2 |
| 38 | Read Distribution | toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/5.0.1+galaxy2 |
| 39 | gffread | toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.3+galaxy0 |
| 40 | StringTie merge | toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.2.1+galaxy1 |
| 41 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1 |
| 42 | rnaQUAST | toolshed.g2.bx.psu.edu/repos/iuc/rnaquast/rna_quast/2.2.3+galaxy0 |
| 43 | gffread | toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.3+galaxy0 |
| 44 | StringTie | toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.1+galaxy1 |
| 45 | Filter collection | __FILTER_FROM_FILE__ |
| 46 | IsoformSwitchAnalyzeR | toolshed.g2.bx.psu.edu/repos/iuc/isoformswitchanalyzer/isoformswitchanalyzer/1.20.0+galaxy5 |
| 47 | IsoformSwitchAnalyzeR | toolshed.g2.bx.psu.edu/repos/iuc/isoformswitchanalyzer/isoformswitchanalyzer/1.20.0+galaxy5 |
| 48 | CPAT | toolshed.g2.bx.psu.edu/repos/bgruening/cpat/cpat/3.0.4+galaxy0 |
| 49 | PfamScan | toolshed.g2.bx.psu.edu/repos/bgruening/pfamscan/pfamscan/1.6+galaxy0 |
| 50 | Remove beginning | Remove beginning1 |
| 51 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2 |
| 52 | Concatenate datasets | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1 |
| 53 | IsoformSwitchAnalyzeR | toolshed.g2.bx.psu.edu/repos/iuc/isoformswitchanalyzer/isoformswitchanalyzer/1.20.0+galaxy5 |
| 54 | IsoformSwitchAnalyzeR | toolshed.g2.bx.psu.edu/repos/iuc/isoformswitchanalyzer/isoformswitchanalyzer/1.20.0+galaxy5 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| lncRNA sequences | lncRNA sequences | n/a |
|
| protein coding sequences | protein coding sequences | n/a |
|
Version History
14 (earliest) Created 22nd Apr 2024 at 11:09 by Helena Rasche
Added/updated 3 files
Open
master1abde75
Creators and Submitter
Activity
Views: 52
Created: 22nd Apr 2024 at 11:09
Last updated: 22nd Apr 2024 at 11:09
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
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
