Tuto Galaxy 2013 : CPB2012 - BasicProtocol3 - Calling Peaks for ChIP-seq Data

Created: 2014-02-27 11:45:22 Last updated: 2014-06-10 09:08:52

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Workflow used when applying the CPB2012 Basic Protocol 3 tutorial from Galaxy team. It calls peaks for ChIP-seq data using MACS14.

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Inputs (2)

Name	Description
Tag File
Control File

Steps (7)

Name	Tool	Description
Input dataset	None
Input dataset	None
FASTQ Groomer	fastq_groomer
FASTQ Groomer	fastq_groomer
Map with Bowtie for Illumina	toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.2
Map with Bowtie for Illumina	toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.2
MACS14	toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/peakcalling_macs14/1.4.1

Outputs (18)

Name	Type
output_file	fastqsanger
output_file	fastqsanger
output	sam
output_suppressed_reads_l	fastq
output_suppressed_reads_r	fastq
output_unmapped_reads_l	fastq
output_unmapped_reads_r	fastq
output	sam
output_suppressed_reads_l	fastq
output_suppressed_reads_r	fastq
output_unmapped_reads_l	fastq
output_unmapped_reads_r	fastq
output_bed_file	bed
output_xls_to_interval_peaks_file	interval
output_xls_to_interval_negative_peaks_file	interval
output_treatment_wig_file	wig
output_control_wig_file	wig
output_extra_files	html

Information Workflow Type

Galaxy

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Ylebras

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Information Version 1 (of 1)

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Ylebras

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Information Statistics

962 viewings

577 downloads

[ see breakdown ]

Citations (1)Version History

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

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