Circos for E. Coli 1.0
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Run on GalaxyThis workflow will create a simple plot of a microbial sized genome (e.g. E. coli) using a couple of datasets like sequencing depth (bigwigs), gff3 formatted annotations, and some variants.
Associated Tutorial
This workflows is part of the tutorial Ploting a Microbial Genome with Circos, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Helena Rasche
Tutorial Author(s): Helena Rasche
Tutorial Contributor(s): Björn Grüning, Saskia Hiltemann
Grants(s): Gallantries: Bridging Training Communities in Life Science, Environment and Health
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| DNA Sequencing Coverage | DNA Sequencing Coverage | n/a |
|
| Genes | Genes | n/a |
|
| Genome | Genome | n/a |
|
| RNA Seq Coverage (1) | RNA Seq Coverage (1) | n/a |
|
| RNA Seq Coverage (2) | RNA Seq Coverage (2) | n/a |
|
| Variants | Variants | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 10 | Circos: bigWig to Scatter | toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy9 |
| 11 | Circos: bigWig to Scatter | toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy9 |
| 12 | Cut | Cut1 |
| 13 | Circos: bigWig to Scatter | toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy9 |
| 14 | Circos: Interval to Tiles | toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_tile/0.69.8+galaxy9 |
| 15 | Circos | toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy9 |
| 6 | GC Skew | toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_gc_skew/0.69.8+galaxy9 |
| 7 | Circos: Interval to Circos Text Labels | toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_interval_to_text/0.69.8+galaxy9 |
| 8 | GFF-to-BED | gff2bed1 |
| 9 | Circos: bigWig to Scatter | toolshed.g2.bx.psu.edu/repos/iuc/circos/circos_wiggle_to_scatter/0.69.8+galaxy9 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| plot | plot | n/a |
|
Version History
master
Creators and Submitter
Views: 1313 Downloads: 190 Runs: 0
Created: 2nd Jun 2025 at 10:52
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Teams: Galaxy Training Network
Organizations: Galaxy
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