Circos for E. Coli
1.0

Workflow Type: Galaxy

This 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 Circos for E. Coli, available in the GTN

Features

Includes Galaxy Workflow Tests

Thanks to...

Tutorial Author(s): Helena Rasche

Workflow Author(s): Helena Rasche

Funder(s): Gallantries: Bridging Training Communities in Life Science, Environment and Health

SEEK ID: https://dev.workflowhub.eu/workflows/1253?version=1

Inputs

ID	Name	Description	Type
DNA Sequencing Coverage	DNA Sequencing Coverage	n/a	File
Genes	Genes	n/a	File
Genome	Genome	n/a	File
RNA Seq Coverage (1)	RNA Seq Coverage (1)	n/a	File
RNA Seq Coverage (2)	RNA Seq Coverage (2)	n/a	File
Variants	Variants	n/a	File

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	File

Version History

1.0 (earliest) Created 25th Jun 2024 at 11:15 by Helena Rasche

Added/updated 4 files

Open master 974731e

Creators and Submitter

Creators

Not specified

Submitter

Helena Rasche

Discussion Channel

GTN Matrix

Tools

Circos

Galactic Circos

License

GNU Affero General Public License v3.0 or later

Activity

Views: 333 Downloads: 74

Created: 25th Jun 2024 at 11:15

Last updated: 25th Jun 2024 at 11:15

Circos for E. Coli 1.0