CRUNCH results

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

Caution:

Crunch is not able to conduct motif analysis as not enough peaks (<200) were called to meaningfully analyse them. Supposedly low input data quality.
The significance level of Crunch can be lowered by increasing the false discovery rate (FDR) under the "Advanced options" menu.

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 peak in peak_lines %} {% 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)
{{peak.chrom}}:{{peak.start}}..{{peak.stop}} {{peak.score}} {{peak.upstream_genes}} {{peak.upstream_offset}} {{peak.downstream_genes}} {{peak.downstream_offset}}

Downloads

Download Peaks (with annotations)
Download Detailed Report PDF about Peak Calling {% 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 %}