NGS : Group and filter mapped reads

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

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Filter and group reads from a mapping Bam file

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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)

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None

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Information Statistics

938 viewings

647 downloads

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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

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