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‎.test/README.md‎

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## Test data
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2 mouse samples:
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* iCre_D0
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* D4_Meso_iCre_Dox
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- iCre_D0
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- D4_Meso_iCre_Dox
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Each sample has 2 replicates. Each replicate has been subsampled to only include reads aligning to chr19:10,000,000-20,000,000
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Each sample has 2 replicates. Each replicate has been subsampled to only include reads aligning to chr19:10,000,000-20,000,000

‎README.md‎

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# ASPEN
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**A**tac **S**eq **P**ip**E**li**N**e :
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**A**tac **S**eq **P**ip**E**li**N**e :
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[CCBR](https://bioinformatics.ccr.cancer.gov/ccbr/) recommends ASPEN to effectively analyze ATAC-seq datasets on the [BIOWULF](https://hpc.nih.gov) HPC system at the [NIH](https://www.nih.gov/).
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```bash
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module load ccbrpipeliner/7
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```
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```bash
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aspen --help
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```

‎config/README.md‎

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## Config files
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* `config.yaml`: sets all the runtime configurations for the pipeline like output folder, resources folder, genome, tool-parameters etc.
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* `samples.tsv`: tab delimited sample manifest. Defaults to the samples in the .test folder of the pipeline
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* `multiqc_atacseq_config.yaml`: custom-multiqc config file for report generation
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* `create_test_config_sample_manifest_files.bash`: replicates variables `PIPELINE_HOME` and `WORKDIR` etc. to create sample manifest for testing purposes
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- `config.yaml`: sets all the runtime configurations for the pipeline like output folder, resources folder, genome, tool-parameters etc.
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- `samples.tsv`: tab delimited sample manifest. Defaults to the samples in the .test folder of the pipeline
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- `multiqc_atacseq_config.yaml`: custom-multiqc config file for report generation
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- `create_test_config_sample_manifest_files.bash`: replicates variables `PIPELINE_HOME` and `WORKDIR` etc. to create sample manifest for testing purposes

‎config/multiqc_atacseq_config.yaml‎

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custom_data:
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Nreads:
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section_name: 'Nreads'
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description: 'Number of reads per replicate. Mitochondrial fraction should be < 10%.'
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nrf_stats:
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file_format: 'tsv'
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section_name: 'NRF PBC Stats'
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description: '
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Non-redundant Fraction (NRF): Number of distinct uniquely mapping reads (i.e. after removing duplicates) / Total number of reads.
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PCR Bottlenecking Coefficient 1 (PBC1): (number of genomic locations where exactly one read maps uniquely) / (number of distinct genomic locations to which some read maps uniquely).
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PCR Bottlenecking Coefficient 2 (PBC2): (number of genomic locations where only one read maps uniquely) / (number of genomic locations where two reads map uniquely).
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The preferred values are as follows: NRF>0.9, PBC1>0.9, and PBC2>3. '
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plot_type: 'table'
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pconfig:
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id: 'NRF Stats'
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title: 'NRF Stats table'
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fld_files:
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file_format: 'tsv'
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section_name: 'Fragment Length Distribution'
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description: 'Per sample FLD. Peak < 150bp = Nucleosome Free Peak, Peak between 150-300 bp = Mononucleosome Peak, Peak > 300bp = Dinucleosome Peak'
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plot_type: 'linegraph'
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pconfig:
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id: 'FLD'
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title: 'Fragment Length Distribution'
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ylab: 'Normalized read density X 1e3'
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xlab: 'Fragment Length'
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xmax: 1000
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fld_stats_peaks:
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file_format: 'tsv'
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section_name: 'FLD Stats (Peaks)'
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description: 'Presence or Absense of nucleosome-free, mono and di-nucleosome peaks in FLD. A nucleosome free region (NFR) must be present. A mononucleosome peak must be present.'
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plot_type: 'table'
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pconfig:
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id: 'FLD Stats'
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title: 'FLD Stats table'
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fld_stats_details:
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file_format: 'tsv'
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section_name: 'FLD Stats (Fractions and Ratios)'
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description: 'Fractions and Ratios of interest'
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plot_type: 'table'
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pconfig:
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id: 'FLD Stats'
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title: 'FLD Stats table'
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MACS2_Peak_Annotations:
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section_name: 'MACS2 Peaks'
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description: 'Peaks called using MACS2. For human or mouse data, Npeaks should be >150,000, though values >100,000 may be acceptable. '
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Genrich_Peak_Annotations:
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section_name: 'Genrich Peaks'
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description: 'Peaks called using Genrich. For human or mouse data, Npeaks should be >150,000, though values >100,000 may be acceptable. '
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peak_width_files:
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file_format: 'tsv'
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section_name: 'Peak width distribution'
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description: 'Peak width distribution of consensus peaks.'
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plot_type: 'linegraph'
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pconfig:
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id: 'PWD'
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title: 'Peak Width Distribution'
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ylab: 'Peak Density Percentage'
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xlab: 'Peak Width'
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xmax: 20000
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frip_stats:
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file_format: 'tsv'
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section_name: 'FRiP Stats'
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description: 'The fraction of reads in called peak regions (FRiP score) should be >0.3, though values greater than 0.2 are acceptable. Fraction of Reads in Peaks/DHS/Enhancers/Promoters are also reported. For human or mouse data, FRiPromoters is 12-20%'
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plot_type: 'table'
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pconfig:
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id: 'FRiP Stats'
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title: 'FRiP Stats table'
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tss_files:
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file_format: 'tsv'
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section_name: 'TSS distribution'
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description: 'Greenleaf Normalized TSS per sample distribution'
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plot_type: 'linegraph'
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pconfig:
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id: 'TSS Enrichment'
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title: 'TSS Enrichment Distribution'
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ylab: 'Greenleaf Normalized TSS Enrichment'
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xlab: 'Distance from TSS'
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tss_knicking_sites_files:
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file_format: 'tsv'
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section_name: 'TSS Score Scatter'
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description: 'TSS score to TSS with >20 Tn5knicking sites scatter. '
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plot_type: 'scatter'
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pconfig:
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id: 'TSS_scatter'
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title: 'TSS_Score_Scatter'
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ylab: 'TSS score'
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xlab: 'Number of TSS sites with > 20 Tn5 knick sites'
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Nreads:
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section_name: "Nreads"
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description: "Number of reads per replicate. Mitochondrial fraction should be < 10%."
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nrf_stats:
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file_format: "tsv"
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section_name: "NRF PBC Stats"
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description: "
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Non-redundant Fraction (NRF): Number of distinct uniquely mapping reads (i.e. after removing duplicates) / Total number of reads.
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PCR Bottlenecking Coefficient 1 (PBC1): (number of genomic locations where exactly one read maps uniquely) / (number of distinct genomic locations to which some read maps uniquely).
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PCR Bottlenecking Coefficient 2 (PBC2): (number of genomic locations where only one read maps uniquely) / (number of genomic locations where two reads map uniquely).
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The preferred values are as follows: NRF>0.9, PBC1>0.9, and PBC2>3. "
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plot_type: "table"
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pconfig:
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id: "NRF Stats"
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title: "NRF Stats table"
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fld_files:
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file_format: "tsv"
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section_name: "Fragment Length Distribution"
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description: "Per sample FLD. Peak < 150bp = Nucleosome Free Peak, Peak between 150-300 bp = Mononucleosome Peak, Peak > 300bp = Dinucleosome Peak"
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plot_type: "linegraph"
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pconfig:
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id: "FLD"
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title: "Fragment Length Distribution"
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ylab: "Normalized read density X 1e3"
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xlab: "Fragment Length"
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xmax: 1000
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fld_stats_peaks:
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file_format: "tsv"
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section_name: "FLD Stats (Peaks)"
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description: "Presence or Absense of nucleosome-free, mono and di-nucleosome peaks in FLD. A nucleosome free region (NFR) must be present. A mononucleosome peak must be present."
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plot_type: "table"
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pconfig:
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id: "FLD Stats"
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title: "FLD Stats table"
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fld_stats_details:
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file_format: "tsv"
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section_name: "FLD Stats (Fractions and Ratios)"
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description: "Fractions and Ratios of interest"
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plot_type: "table"
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pconfig:
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id: "FLD Stats"
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title: "FLD Stats table"
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MACS2_Peak_Annotations:
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section_name: "MACS2 Peaks"
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description: "Peaks called using MACS2. For human or mouse data, Npeaks should be >150,000, though values >100,000 may be acceptable. "
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Genrich_Peak_Annotations:
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section_name: "Genrich Peaks"
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description: "Peaks called using Genrich. For human or mouse data, Npeaks should be >150,000, though values >100,000 may be acceptable. "
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peak_width_files:
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file_format: "tsv"
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section_name: "Peak width distribution"
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description: "Peak width distribution of consensus peaks."
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plot_type: "linegraph"
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pconfig:
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id: "PWD"
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title: "Peak Width Distribution"
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ylab: "Peak Density Percentage"
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xlab: "Peak Width"
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xmax: 20000
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frip_stats:
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file_format: "tsv"
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section_name: "FRiP Stats"
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description: "The fraction of reads in called peak regions (FRiP score) should be >0.3, though values greater than 0.2 are acceptable. Fraction of Reads in Peaks/DHS/Enhancers/Promoters are also reported. For human or mouse data, FRiPromoters is 12-20%"
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plot_type: "table"
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pconfig:
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id: "FRiP Stats"
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title: "FRiP Stats table"
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tss_files:
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file_format: "tsv"
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section_name: "TSS distribution"
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description: "Greenleaf Normalized TSS per sample distribution"
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plot_type: "linegraph"
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pconfig:
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id: "TSS Enrichment"
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title: "TSS Enrichment Distribution"
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ylab: "Greenleaf Normalized TSS Enrichment"
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xlab: "Distance from TSS"
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tss_knicking_sites_files:
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file_format: "tsv"
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section_name: "TSS Score Scatter"
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description: "TSS score to TSS with >20 Tn5knicking sites scatter. "
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plot_type: "scatter"
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pconfig:
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id: "TSS_scatter"
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title: "TSS_Score_Scatter"
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ylab: "TSS score"
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xlab: "Number of TSS sites with > 20 Tn5 knick sites"
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sp:
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nrf_stats:
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fn: 'NRF_stats.tsv'
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frip_stats:
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fn: 'FRiP_stats.tsv'
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fld_stats_peaks:
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fn: 'FLD_stats_peaks.tsv'
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fld_stats_details:
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fn: 'FLD_stats_fractions_ratios.tsv'
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tss_knicking_sites_files:
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fn: 'data.tss_nicking_sites.txt'
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peak_width_files:
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fn: '*.annotated.peak_width_density'
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fld_files:
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fn: '*.fld.txt'
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tss_files:
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fn: '*.tss.txt'
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nrf_stats:
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fn: "NRF_stats.tsv"
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frip_stats:
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fn: "FRiP_stats.tsv"
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fld_stats_peaks:
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fn: "FLD_stats_peaks.tsv"
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fld_stats_details:
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fn: "FLD_stats_fractions_ratios.tsv"
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tss_knicking_sites_files:
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fn: "data.tss_nicking_sites.txt"
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peak_width_files:
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fn: "*.annotated.peak_width_density"
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fld_files:
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fn: "*.fld.txt"
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tss_files:
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fn: "*.tss.txt"
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fn_clean_exts:
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- '.genrich.narrowPeak.annotation_distribution'
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- '.consensus.bed.annotated.peak_width_density'
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- '.filt.bam'
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- '.preseq'
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- '.tss.txt'
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- '.fld.txt'
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- '.bowtie2.log'
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- '.fastq.gz'
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- ".genrich.narrowPeak.annotation_distribution"
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- ".consensus.bed.annotated.peak_width_density"
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- ".filt.bam"
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- ".preseq"
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- ".tss.txt"
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- ".fld.txt"
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- ".bowtie2.log"
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- ".fastq.gz"

‎docs/css/custom.css‎

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/* Light blue background for notes */
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div.admonition.note {
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background-color: #e3f2fd;
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border-left: 5px solid #2196F3;
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border-left: 5px solid #2196f3;
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padding: 10px;
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margin: 10px 0;
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border-radius: 5px;
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/* Light grey background for info */
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div.admonition.info {
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background-color: #f5f5f5;
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border-left: 5px solid #9E9E9E;
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border-left: 5px solid #9e9e9e;
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padding: 10px;
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margin: 10px 0;
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border-radius: 5px;
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/* Orange warning box */
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div.admonition.warning {
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background-color: #fff3e0;
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border-left: 5px solid #FF9800;
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border-left: 5px solid #ff9800;
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padding: 10px;
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margin: 10px 0;
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border-radius: 5px;
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}
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