CRUNCH results

CRUNCH Results {% if project != '' %} for {{ project }}{% endif %}

Quality Control, Mapping, Fragment Size Estimation:

{% for rep in samples %} {% if rep.file_type == "shiftedbed" -%}

{{rep.name}}

  • {{rep.num_reads_input}} input reads (in BED format, shifted by half of fragment size).
  • Report PDF
{% elif rep.file_type == "bed" -%}

{{rep.name}}

fragment size plot
  • {{rep.num_reads_input}} input reads (in BED format).
  • Report PDF
{% elif rep.file_type == "fasta" -%}

{{rep.name}}

fragment size plot
  • {{rep.num_reads_input}} input reads (in FASTA format).
  • {{rep.num_reads_2QC}} reads after removal of adapters and low complexity reads.
  • {{rep.num_reads_mapped}} reads after mapping.
  • Report PDF
{% elif rep.file_type == "fastq" -%}

{{rep.name}}

fragment size plot
  • {{rep.num_reads_input}} input reads (in FASTQ format).
  • {{rep.num_reads_1QC}} reads after removal of low quality reads.
  • {{rep.num_reads_2QC}} reads after removal of adapters and low complexity reads.
  • {{rep.num_reads_mapped}} reads after mapping.
  • Report PDF
{% endif %} {% endfor %}

Peak Calling:

zvalue histogram reverse cumulative of zvalues

Top peaks:

{% if organism == "dm3" -%} {% else %} {% endif %} {% if organism == "dm3" -%} {% else %} {% endif %} {% for name in motif_names %} {% endfor %} {% for peak in peak_lines %} {% for name in motif_names %} {% for key, value in peak.sites.iteritems() %} {% if key == name -%} {% endif %} {% endfor %} {% endfor %} {% endfor %}
Coordinates Z-score Nearest Genes on the LeftOffset of Nearest Genes on the Left (Strand)Offset of Nearest TSS on the Left (Strand)Nearest Genes on the RightOffset of Nearest Genes on the Right (Strand)Offset of Nearest TSS on the Right (Strand){{name}}
{{peak.chrom}}:{{peak.start}}..{{peak.stop}} {{peak.score}} {{peak.upstream_genes}} {{peak.upstream_offset}} {{peak.downstream_genes}} {{peak.downstream_offset}}

{{value}}

Complementary Motifs Enriched In Peaks:

{% for motif in motif_list %} {% endfor %}

Motif Name

Sequence Logo

Motif Ensemble Enrichment (Motif Ensemble log-Likelihood Ratio)

Enrichment (log-Likelihood Ratio)

Precision and Recall

Prediction - Observation Correlation

Enrichment at Binding Sites

Number of Positively Predicted Peaks
{{motif.name_unquote}} {{motif.ensemble_score}} ({{motif.ensemble_LLratio}}) {{motif.score}} ({{motif.LLratio}}) {{motif.auc}} {{motif.fov}} {{motif.eabs}} {{motif.truepeaks}}

Top Motifs Enriched In Peaks:

{% for motif in motif_tops_list %} {% endfor %}

Motif Name

Sequence Logo

Enrichment (log-Likelihood Ratio)

Precision and Recall

Prediction - Observation Correlation

Enrichment at Binding Sites

Number of Positively Predicted Peaks
{{motif.name_unquote}} {{motif.score}} ({{motif.LLratio}}) {{motif.auc}} {{motif.fov}} {{motif.eabs}} {{motif.truepeaks}}

Downloads

{% for rep in samples %} {% if rep.file_type == "shiftedbed" -%}

{{rep.name}}

{% elif rep.file_type == "bed" -%}

{{rep.name}}

{% elif rep.file_type == "fasta" -%}

{{rep.name}}

{% elif rep.file_type == "fastq" -%}

{{rep.name}}

{% endif %} {% endfor %}