Category
Genome Annotation
Usage
pints_caller --file-prefix FILE_PREFIX --bam-file [BAM_FILE ...] [--exp-type GROcap,etc.]
Manual
This command identifies transcriptional regulatory elements (TREs, enhancers and promoters) from Transcription Start Site (TSS) assays
Options
- Input/Output:
- --bam-file [BAM_FILE ...]: input bam file
- --save-to SAVE_TO: save peaks to this path (a folder), by default, current folder
- --file-prefix FILE_PREFIX: prefix to all intermediate files
- --ct-bam [CT_BAM ...]: Bam file for input/control (minus strand).
- --exp-type {CoPRO,GROcap,PROcap,CAGE,NETCAGE,RAMPAGE,csRNAseq,STRIPEseq,PROseq,GROseq,R_5,R_3,R1_5,R1_3,R2_5,R2_3}: Type of experiment. If the experiment is not listed as a choice, or you know the position of RNA ends on the reads and you want to override the defaults, you can specify:
- R_5 (5' of the read for single-end lib)
- R_3 (3' of the read for single-end lib)
- R1_5 (5' of the read1 for paired-end lib)
- R1_3 (3' of the read1 for paired-end lib)
- R2_5 (5' of the read2 for paired-end lib)
- R2_3 (3' of the read2 for paired-end lib)
- --reverse-complement: Set this switch if reads in this library represent the reverse complement of RNAs, like PROseq
- -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
- --mapq-threshold MAPQ_THRESHOLD: Minimum mapping quality. By default 30
- --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 a GRO-cap library.
pints_caller --bam-file GROcap_hg38.uniq.bam \
--exp-type GROcap \
--file-prefix GROcap_hg38 \
--filters U13369 chrM EBV \
--thread 8
If you have two strand specific bigwig files instead of a bam file, you can directly use PINTS with bigwig inputs
.
This document is generated with PINTS version 1.1.8.
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