NGS : Group and filter mapped reads

Created: 2014-03-05 10:53:15 Last updated: 2014-06-10 09:06:30

Download Workflow

Filter and group reads from a mapping Bam file

Preview

Download as scalable diagram (SVG)

Import

Not currently available.

Workflow Components

Inputs (2)

Name	Description
Reference genome
BAM file

Steps (10)

Name	Tool	Description
Input dataset	None
Input dataset	None
Generate pileup	toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.1
BAM-to-SAM	toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/1.0.3
Group	Grouping1
Filter	testtoolshed.g2.bx.psu.edu/repos/greg/gregs_filter/Filter1/3.3.0
Join two Datasets	join1
Group	Grouping1
Filter	testtoolshed.g2.bx.psu.edu/repos/greg/gregs_filter/Filter1/3.3.0
Group	Grouping1

Outputs (8)

Name	Type
output1	tabular
output1	sam
out_file1	tabular
out_file1	input
out_file1	input
out_file1	tabular
out_file1	input
out_file1	tabular

Information Workflow Type

Galaxy

Information Uploader

Ylebras

Information License

All versions of this Workflow are licensed under:

Information Version 1 (of 1)

Information Credits (1)

(People/Groups)

Ylebras

Information Attributions (0)

(Workflows/Files)

None

Information Tags (3)

Uploader tags

Log in to add Tags

Information Shared with Groups (0)

None

Information Featured In Packs (0)

None

Log in to add to one of your Packs

Information Attributed By (0)

(Workflows/Files)

None

Information Favourited By (0)

No one

Information Statistics

911 viewings

621 downloads

[ see breakdown ]

Citations (1)

1. Y. Le Bras, A. Roult, C. Monjeaud, M. Bahin, O. Quenez, C. Heriveau, A. Bretaudeau, O. Sallou, O. Collin, Towards a Life Sciences Virtual Research Environment : an e-Science initiative in Western France, JOBIM 2013, 03 July 2013, https://www.e-biogenouest.org/resources/128

Version History

In chronological order: