pints_caller

Reference Code backup Executable files

Identify transcriptional regulatory elements (enhancers and promoters) from sequencing libraries of transcription start site assays

Category

Genome Annotation

Usage

pints_caller --file-prefix FILE_PREFIX --bw-pl [BW_PL ...] --bw-mn [BW_MN ...]

Manual

This command identifies transcriptional regulatory elements (TREs, enhancers and promoters) from Transcription Start Site (TSS) assays

Options

  • Input/Output:
    • --save-to SAVE_TO: save peaks to this path (a folder), by default, current folder
    • --file-prefix FILE_PREFIX: prefix to all intermediate files
    • --bw-pl [BW_PL ...]: Bigwig for plus strand.
    • --bw-mn [BW_MN ...]: Bigwig for minus strand.
    • --ct-bw-pl [CT_BW_PL ...]: Bigwig for control/input (plus strand).
    • --ct-bw-mn [CT_BW_MN ...]: Bigwig for input/control (minus strand).
    • -f [FILTERS ...], --filters [FILTERS ...]: reads from chromosomes whose names contain any matches in filters will be ignored
  • Filtering:
    • --adjust-method {fdr_bh,bonferroni,fdr_tsbh,fdr_tsbky}: method for calculating adjusted p-values. By default fdr_bh
    • --fdr-target FDR_TARGET: FDR target for multiple testing. By default 0.1
    • --close-threshold CLOSE_THRESHOLD: Distance threshold for two peaks (on opposite strands) to be merged. By default 1
    • --stringent-pairs-only: Only consider elements as bidirectional when both of the two peaks are significant according to their p-values
    • --min-length-opposite-peaks MIN_LEN_OPPOSITE_PEAKS, --min-lengths-opposite-peaks MIN_LEN_OPPOSITE_PEAKS: Minimum length requirement for peaks on the opposite strand to be paired, set it to 0 to loose this requirement. By default 0
    • --small-peak-threshold SMALL_PEAK_THRESHOLD: Threshold for small peaks, peaks with width smaller than this value will be required to run extra test. By default 5
    • --max-window-size WINDOW_SIZE_THRESHOLD: max size of divergent windows. By default 2000
    • --remove-sticks: Set this switch to remove stick-like peaks (signal on a single position)
  • Edge trimming:
    • --annotation-gtf ANNOTATION_GTF: Gene annotation file (gtf) format for learning the threshold for edge trimming. If this is specified, other related parameters like --donor-tolerance will be ignored.
    • --tss-extension TSS_EXTENSION: BPs to be extended from annotated TSSs, these extended regions will be used to minimize overlaps between called peaks. By default 200
    • --focused-chrom FOCUSED_CHROM: If --annotation-gtf is specified, you use this parameter to change which chromosome the tool should learn the values from. By default chr1
    • --alpha DONOR_TOLERANCE, --donor-tolerance DONOR_TOLERANCE: The stringency for PINTS to cluster nearby TSSs into a peak. 0 is the least stringent; 1 is the most stringent. By default 0.3
    • --ce-trigger CE_TRIGGER: Trigger for receptor tolerance checking. By default 3
  • Peak properties:
    • --top-peak-threshold TOP_PEAK_THRESHOLD: For very short peaks (smaller than --small-peak-threshold), we use the quantile threshold for peak densities as the background density. By default 0.75.
    • --min-mu-percent MIN_MU_PERCENT: Local backgrounds smaller than this percentile among all peaks will be replaced. By default 0.1. Starting from version 1.1.7, this value will be automatically adjusted.
    • --peak-distance PEAK_DISTANCE: Peaks within this distance (>= 1) will be joined together. By default 1.
    • --peak-width PEAK_WIDTH: Required width of peaks in samples. By default None (no limits)
    • --div-size-min DIV_SIZE_MIN: Min size for a divergent peak. By default 0
    • --summit-dist-min SUMMIT_DIST_MIN: Min dist between two summit. By default 0
  • Testing:
    • --model {ZIP,Poisson}: Statistical model for testing the significance of peaks. By default ZIP
    • --IQR-strategy {bgIQR,pkIQR}: IQR strategy, can be bgIQR (more robust) or pkIQR (more efficient). By default bgIQR
    • --disable-ler: Disable Local Environment Refinement
    • --disable-eler: Disable Enhanced Local Environment Refinement
    • --eler-lower-bound ELER_LOWER_BOUND: Lower bound of the empirical estimation for the density of potential true peaks in the local background. By default 1
    • --disable-small: Set this switch to prevent PINTS from reporting very short peaks(shorter than --small-peak-threshold)
  • Other:
    • --epig-annotation EPIG_ANNOTATION: Refine peak calls with compiled epigenomic annotation from the PINTS web server. Values should be the name of the biosample, for example, K562.
    • --relaxed-fdr-target RELAXED_FDR_TARGET: Relaxed FDR cutoff for TREs overlap with epigenomic annotations. By default 0.2
    • --thread THREAD_N: Max number of threads PINTS can create. By default 1
    • --chromosome-start-with CHROMOSOME_STARTSWITH: Only keep reads mapped to chromosomes with this prefix
    • --dont-output-chrom-size: Don't write chromosome dict to local folder (not recommended)
    • --dont-check-updates: Set this switch to disable update check.
    • --disable-qc: Disable on-the-fly quality control
    • --strict-qc: Raise exceptions if PINTS detects abnormalities during on-the-fly quality control; otherwise, PINTS prints warning messages.
    • --debug: Save diagnostics (independent filtering and pval dist) to local folder
    • --dont-borrow-info-reps: Don't borrow information from reps to refine calling of divergent elements

Example

Real case studies are available at the PINTS web portal. Here is one example using pints_caller to identify TREs from strand specific bigwigs.

pints_caller --bw-pl GROcap_hg38_pl.bw \  # signal on the forward strand
    --bw-mn GROcap_hg38_mn.bw \. # signal on the reverse strand
    --file-prefix GROcap_hg38 \
    --thread 8

If you have a bam file instead of strand specific bigwig files, you can directly use PINTS with bam inputs or use PINTS visualizer to convert the bam file to strand specific bigwigs first, then use this command.

This document is generated with PINTS version 1.1.8.

Protocols using this tool

PROcap preprocessing (with two replicates)

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