NGS : Coverage determination and visualization

Created: 2014-02-28 10:51:49 Last updated: 2014-06-10 09:22:11

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From a BAM file and a reference genome fasta file, calculate the depth of coverage and generate pileup, interval, Base coverage as Summary statistics

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Workflow Components

Inputs (3)

Name	Description
BAM file
Reference genome
Input Dataset

Steps (10)

Name	Tool	Description
Input dataset	None
Input dataset	None
Input dataset	None
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
Base Coverage	gops_basecoverage_1

Outputs (32)

Name	Type
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
output	txt

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Galaxy

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Ylebras

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Information Statistics

859 viewings

606 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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