Workflow Type: Galaxy
Open
Frozen
Training workflow
Associated Tutorial
This workflows is part of the tutorial Genome-wide alternative splicing analysis: human, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): Cristóbal Gallardo, Lucille Delisle
Tutorial Contributor(s): Pavankumar Videm
Workflow Author(s): Cristóbal Gallardo Alba
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
2.0 (latest) Created 16th Jul 2024 at 14:06 by Helena Rasche
Added/updated 4 files
Open
master
3acb26d
14.0 (earliest) Created 25th Jun 2024 at 11:24 by Helena Rasche
Added/updated 4 files
Frozen
14.0
539ac6b
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Activity
Views: 197 Downloads: 77
Created: 25th Jun 2024 at 11:24
Last updated: 25th Jun 2024 at 11:24
![help](/assets/famfamfam_silk/information-8cfe563be76fb11b27c8ba778f5d40ce6800b244d6ca58ef6e9973308efbe534.png)
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