NGS : Bowtie2 with a genome in fasta format to depth of coverage and base coverage

Created: 2014-02-28 10:58:46 Last updated: 2014-06-10 09:14:47

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Reads mapping using a reference genome in fasta format from your history, then generate pileup, base coverage, depth of coverage and summary statistics

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Workflow Components

Inputs (5)

Name	Description
FastQ file
Fasta reference genome
rgpl	runtime parameter for tool Add or Replace Groups
rgsm	runtime parameter for tool Add or Replace Groups
rglb	runtime parameter for tool Add or Replace Groups

Steps (11)

Name	Tool	Description
Input dataset	None
Input dataset	None
Base Coverage	gops_basecoverage_1
Bowtie2	bowtie2
Add or Replace Groups	toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ARRG/1.56.0
Generate pileup	toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.1
Depth of Coverage	gatk_depth_of_coverage
Filter pileup	toolshed.g2.bx.psu.edu/repos/devteam/pileup_parser/pileup_parser/1.0.2
Filter	testtoolshed.g2.bx.psu.edu/repos/greg/gregs_filter/Filter1/3.3.0
Pileup-to-Interval	toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.0
Summary Statistics	Summary_Statistics1

Outputs (36)

Name	Type
output	txt
output_unaligned_reads_l	fastqsanger
output_unaligned_reads_r	fastqsanger
output	bam
outFile	bam
output1	tabular
output_per_locus_coverage	tabular
output_summary_sample	tabular
output_statistics_sample	tabular
output_interval_summary_sample	tabular
output_interval_statistics_sample	tabular
output_gene_summary_sample	tabular
output_gene_statistics_sample	tabular
output_cumulative_coverage_counts_sample	tabular
output_cumulative_coverage_proportions_sample	tabular
output_summary_readgroup	tabular
output_statistics_readgroup	tabular
output_interval_summary_readgroup	tabular
output_interval_statistics_readgroup	tabular
output_gene_summary_readgroup	tabular
output_gene_statistics_readgroup	tabular
output_cumulative_coverage_counts_readgroup	tabular
output_cumulative_coverage_proportions_readgroup	tabular
output_summary_library	tabular
output_statistics_library	tabular
output_interval_summary_library	tabular
output_interval_statistics_library	tabular
output_gene_summary_library	tabular
output_gene_statistics_library	tabular
output_cumulative_coverage_counts_library	tabular
output_cumulative_coverage_proportions_library	tabular
output_log	tabular
out_file1	tabular
out_file1	input
output	tabular
out_file1	tabular

Information Workflow Type

Galaxy

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Ylebras

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Ylebras

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Information Statistics

1048 viewings

676 downloads

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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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