Peak calling

This report is based

Failed IDR

[% failed_idrs = idr_adaptor.fetch_all_failed %]

The IDR failed in [% failed_idrs.size %] instances.

[% FOR failed_idr IN failed_idrs %] [% END %]
Experiment Epigenome Type Error message
[% failed_idr.fetch_Experiment.name %] [% failed_idr.fetch_Experiment.epigenome.display_label %] [% failed_idr.type %] [% failed_idr.failed_idr_pairs %]

Failed peak callings

[% failed_peak_callings = peak_calling_adaptor.fetch_all_failed %]

Peak calling failed in [% failed_peak_callings.size %] instances.

[% FOR failed_peak_calling IN failed_peak_callings %] [% END %]
Name Feature type Broad peaks Epigenome Error message
[% failed_peak_calling.name %] [% failed_peak_calling.fetch_FeatureType.name %] [% boolean_to_yes_no( failed_peak_calling.fetch_FeatureType._creates_broad_peaks ) %] [% failed_peak_calling.fetch_Epigenome.display_label %] [% failed_peak_calling.error_message%]

Proportion of genome in peaks by feature type and epigenome in percent (0-100)

[%- FOR current_feature_type IN feature_types -%]

[% current_feature_type.name %]

If the [% current_feature_type.name %] peaks from all epigenomes were projected to the genome, they would cover [% round_percent( peak_calling_statistic_adaptor .fetch_coverage_percent_by_FeatureType( current_feature_type ).value ) %]% of the genome.

[% END %]

Peak calling statistics

To compute the proportion of genome in peaks, a genome length of [% format_number( genome_size_in_bp ) %] base pairs was used.

[% FOR peak_calling IN peak_calling_adaptor.fetch_all %] [% END %]
Epigenome Feature type Proportion of genome in peaks Number of peaks Average length
[% peak_calling.fetch_Epigenome.display_label %] [% peak_calling.fetch_FeatureType.name %] [% round_percent( length_to_percent( peak_calling_statistic_adaptor .fetch_by_PeakCalling_total_length( peak_calling, 'total_length' ).value ) ) %] [% format_number( peak_calling_statistic_adaptor .fetch_by_PeakCalling_total_length( peak_calling, 'num_peaks' ).value ) %] [% format_number( peak_calling_statistic_adaptor .fetch_by_PeakCalling_total_length( peak_calling, 'average_length' ).value ) %]

IDR

Signal Experiments

[% FOR experiment IN signal_experiments %] [% idr = fetch_idr(experiment) %] [% END %]
Experiment Feature type Read type Replicate configurations Number of reads Sum of read file sizes in GB Ratio of read counts: signal/control IDR type Max peaks Failed IDR pairs
[% experiment.name %] [% experiment.feature_type.name %] [% experiment.summarise_read_types %] [% experiment.summarise_replicate_configurations %] [% format_number( experiment.sum_number_of_reads ) %] [% format_number( bytes_to_gb ( experiment.sum_read_file_sizes ) ) %] [% round_num( experiment.signal_to_control_read_file_ratio ) %] [% idr.type %] [% format_number( idr.max_peaks ) %] [% idr.failed_idr_pairs %]

Control Experiments

[% FOR experiment IN control_experiments %] [% END %]
Experiment Feature type Read type Replicate configurations Number of reads Sum of read file sizes in GB
[% experiment.name %] [% experiment.feature_type.name %] [% experiment.summarise_read_types %] [% experiment.summarise_replicate_configurations %] [% format_number( experiment.sum_number_of_reads ) %] [% format_number( bytes_to_gb ( experiment.sum_read_file_sizes ) ) %]