Catchitt

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Catchitt is a collection of tools for predicting cell type-specific binding regions of transcription factors (TFs) based on binding motifs and chromatin accessibility assays. The initial implementation of this methodology has been one of the winning approaches of the ENCODE-DREAM challenge ([1]) and is described in a preprint (https://www.biorxiv.org/content/early/2017/12/06/230011 doi: 10.1101/230011). The implementation in Catchitt has been streamlined and slightly simplified to make its application more straight-forward. Specifically, we reduced the set of chromatin accessibility features to the most important ones, we simplified the sampling strategy of initial negative examples in the training step, and we omitted quantile normalization of chromatin accessibility features.

Contents

Catchitt tools

Catchitt comprises five tools for the individual steps of the pipeline (see below). The tool "labels" computes labels for genomic regions from "conservative" (i.e., IDR-thresholded) and "relaxed" ChIP-seq peaks. The tool "access" computes chromatin accessibility features from DNase-seq or ATAC-seq data, either based on fold-enrichment tracks in Bigwig format (e.g., MACS output) or based on SAM/BAM files of mapped reads. The tool "motif" computes motif-based features from genomic sequence and PWMs in Jaspar or HOCOMOCO format, or motif models from Dimont, including Slim models. The tool "itrain" performs iterative training of a series of classifiers based on labels, chromatin accessibility features, and motif features. The tool "predict" predicts binding probabilities of genomic regions based on trained classifiers and feature files. The feature files may either be measured on the training cell type (e.g., other chromosomes, "within cell type" case) or on a different cell type.

Availability

We provide Catchitt as a pre-compiled JAR file and also publish its source code under GPL 3. For compiling Catchitt from source files, Jstacs (v. 2.3 and later) and the corresponding external libraries are required.

Catchitt is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose.

  • JAR download
  • the source code of Catchitt is available from github in package projects.encodedream.

Usage

Catchitt can be started by calling

java -jar Catchitt.jar

on the command line. This lists the names of the available tools with a short description:

Available tools:

	access - Chromatin accessibility
	motif - Motif scores
	labels - Derive labels
	itrain - Iterative Training
	predict - Prediction

Syntax: java -jar Catchitt.jar <toolname> [<parameter=value> ...]

Further info about the tools is given with
	java -jar Catchitt.jar <toolname> info

Tool parameters are listed with
	java -jar Catchitt.jar <toolname>

Tools

Derive labels

Derive labels computes labels for genomic regions based on ChIP-seq peak files. The input ChIP-seq peak files must be provided in narrowPeak format and may come in 'conservative', i.e., IDR-thresholded, and 'relaxed' flavors. In case only a single peak file is available, both of the corresponding parameters may be set to this one peak file. The parameter for the bin width defines the resolution of genomic regions that is assigned a label, while the parameter for the region width defines the size of the regions considered. If, for instance, the bin width is set to 50 and the region width to 100, regions of 100 bp shifted by 50 bp along the genome are labeled. The labels assigned may be 'S' (summit) is the current bin contains the annotated summit of a conservative peak, 'B' (bound) if the current region overlaps a conservative peak by at least half the region width, 'A' (ambiguous) if the current region overlaps a relaxed peak by at least 1 bp, or 'U' (unbound) if it overlaps with none of the peaks. The output is provided as a gzipped file 'Labels.tsv.gz' with columns chromosome, start position, and label. This output file together with a protocol of the tool run is saved to the specified output directory.

Derive labels may be called with

java -jar Catchitt.jar labels

and has the following parameters

name comment type

c Conservative peaks (NarrowPeak file containing the conservative peaks) FILE
r Relaxed peaks (NarrowPeak file containing the relaxed peaks) FILE
f FAI of genome (FastA index file of the genome) FILE
b Bin width (The width of the genomic bins considered, valid range = [1, 10000], default = 50) INT
rw Region width (The width of the genomic regions considered for overlaps, valid range = [1, 10000], default = 50) INT
outdir The output directory, defaults to the current working directory (.) STRING

Example:

java -jar Catchitt.jar labels c=conservative.narrowPeak r=relaxed.narrowPeak f=hg19.fa.fai b=50 rw=200 outdir=labels


Chromatin accessibility

Chromatin accessibility computes several chromatin accessibility features from DNase-seq or ATAC-seq data provided as fold-enrichment tracks or SAM/BAM files of mapped reads. Features a computed with a certain resolution defined by the bin width parameter. Setting this parameter to 50, for instance, features are computed for non-overlapping 50 bp bins along the genome. If input data are provided as SAM/BAM file, coverage information is extracted and normalized locally in a similar fashion as proposed for the MACS peak caller. Output is provided as a gzipped file 'Chromatin_accessibility.tsv.gz' with columns chromosome, start position of the bin, minimum coverage and median coverage in the current bin, minimum coverage in 1000 bp regions before and after the current bin, maximum coverage in 1000 bp regions before and after the current bin, the number of steps in the coverage profile, and the number of monotonically increasing and decreasing steps in the coverage profile of the current bin. This output file together with a protocol of the tool run is saved to the specified output directory.

Chromatin accessibility may be called with

java -jar Catchitt.jar access

and has the following parameters


name comment type

d Data source (The format of the input file containing the coverage information, range={BAM/SAM, Bigwig}, default = BAM/SAM)
Parameters for selection "BAM/SAM":
i Input SAM/BAM (The input file containing the mapped DNase-seq/ATAC-seq reads) FILE
Parameters for selection "Bigwig":
i Input Bigwig (The input file containing the mapped DNase-seq/ATAC-seq reads) FILE
f FastA index (The genome index) FILE
b Bin width (The width of the genomic bins considered) INT
outdir The output directory, defaults to the current working directory (.) STRING

Example:

java -jar Catchitt.jar access d="Bigwig" i=fold_enrich.bw f=hg19.fa.fai b=50 outdir=dnase

Motif scores

Motif scores computes features based on motif scores of a given motif model scanning sub-sequences along the genome. Motif scores are aggregated in bins of the specified width as maximum score and log of the average exponential score (i.e., average log-likelihood in case of statistical models). The motif model may be provided as PWMs in HOCOMOCO or PFMs in Jaspar format, or as Dimont motif models in XML format. For more complex motif models like Slim models, the current implementation uses several indexes to speed-up the scanning process. However, computation of these indexes is rather memory-consuming and often not reasonable for simple PWM models. Hence, a low-memory variant of the tool is available, which is typically only slightly slower for PWM models but substantially slower for Slim models. Output is provided as a gzipped file 'Motif_scores.tsv.gz' containing columns chromosome, start position, maximum and average score. This output file together with a protocol of the tool run is saved to the specified output directory.


Motif scores may be called with

java -jar Catchitt.jar motif

and has the following parameters

name comment type

m Motif model (The motif model in Dimont, HOCOMOCO, or Jaspar format, range={Dimont, HOCOMOCO, Jaspar}, default = Dimont)
Parameters for selection "Dimont":
d Dimont motif (Dimont motif model description) FILE
Parameters for selection "HOCOMOCO":
h HOCOMOCO PWM (PWM from the HOCOMOCO database) FILE
Parameters for selection "Jaspar":
j Jaspar PFM (PFM in Jaspar format) FILE
g Genome (Genome as FastA file) FILE
f FAI of genome (FastA index file of the genome) FILE
b Bin width (The width of the genomic bins considered) INT
l Low-memory mode (Use slower mode with a smaller memory footprint, default = true) BOOLEAN
outdir The output directory, defaults to the current working directory (.) STRING
threads The number of threads used for the tool, defaults to 1 STRING

Example

java -jar Catchitt.jar motif m=HOCOMOCO h=motif.pwm g=hg19.fa f=hg19.fa.fai b=50 outdir=motifs

Iterative Training

Iterative Training performs an iterative training with the specified number of iterations to obtain a series of classifiers that may be used for predictions in the same cell type or in other cell types based on a corresponding set of feature files. The tool requires as input labels for the training chromosomes, a chromatin accessibility feature file and a set of motif feature files. From the labels, an initial set of training regions is extracted containing all positive examples labeled as 'S' (summit) and a sub-sample of negative examples of regions labeled as 'U' (unbound). During the iterations, the initial negative examples are complemented with additional negatives obtaining large binding probabilities, i.e., putative false positive predictions. As these additional negative examples are derived from predictions of the current set of classifiers, the number of bins used for aggregation needs to be specified and should be identical to those used for predictions later. Training chromosomes and chromosomes used for predictions in the iterative training may be specified, as well as the percentile of the scores of positive (i.e., summit or bound regions) that should be used to identify putative false positives. The specified bin width must be identical to the bin width specified when computing the corresponding feature files. Feature vectors for training regions may span several adjacent bins as specified by the bin width parameter. Output is an XML file Classifiers.xml containing the set of trained classifiers. This output file together with a protocol of the tool run is saved to the specified output directory.

Iterative Training may be called with

java -jar Catchitt.jar itrain

and has the following parameters

name comment type

a Accessibility (File containing accessibility features) FILE
m Motif (File containing motif features), MAY BE USED MULTIPLE TIMES FILE
l Labels (File containing the labels) FILE
f FAI of genome (FastA index file of the genome) FILE
b Bin width (The width of the genomic bins, valid range = [1, 1000], default = 50) INT
n Number of bins (The number of adjacent bins, valid range = [1, 20], default = 5) INT
abb Aggregation: bins before (The number of bins before the current one considered in the aggregation, valid range = [1, 20], default = 1) INT
aba Aggregation: bins after (The number of bins after the current one considered in the aggregation, valid range = [1, 20], default = 4) INT
i Iterations (The number of iterations of the interative training, valid range = [1, 20], default = 5) INT
t Training chromosomes (Training chromosomes, separated by commas, OPTIONAL) STRING
itc Iterative training chromosomes (Chromosomes with predictions in iterative training, separated by commas, OPTIONAL) STRING
p Percentile (Percentile of the prediction scores of positives used as threshold in iterative training, valid range = [0.0, 1.0], default = 0.01) DOUBLE
outdir The output directory, defaults to the current working directory (.) STRING
threads The number of threads used for the tool, defaults to 1 STRING

Example

java -jar Catchitt.jar itrain a=dnase/Chromatin_accessibility.tsv.gz m=motif1/Motif_scores.tsv.gz m=motif2/Motif_scores.tsv.gz l=labels/Labels.tsv.gz f=hg19.fa.fai b=50 n=5 abb=1 aba=4 i=5 t="chr1,chr2,chr3" itc="chr1,chr2" p=0.01 outdir=cls

Prediction

Prediction predicts binding probabilities of genomic regions as specified during training of the set of classifiers in iterative training. As input, Prediction requires a set of trained classifiers in XML format, the same (type of) feature files as used in training (motif files must be specified in the same order!). In addition, the chromosomes for which predictions are made may be specified, and the number of bins used for aggregation may be specified to deviate from those used during training. If these bin numbers are not specified, those from the training run are used. Finally, it is possible to restrict the number of classifiers considered to the first n ones. Output is provided as a gzipped file 'Predictions.tsv.gz' with columns chromosome, start position, binding probability. This output file together with a protocol of the tool run is saved to the specified output directory.

Prediction may be called with

java -jar Catchitt.jar predict

and has the following parameters

name comment type

c Classifiers (The classifiers trained by iterative training) FILE
a Accessibility (File containing accessibility features) FILE
m Motif (File containing motif features) MAY BE USED MULTIPLE TIMES FILE
f FAI of genome (FastA index file of the genome) FILE
p Prediction chromosomes (Prediction chromosomes, separated by commas, OPTIONAL) STRING
abb Aggregation: bins before (Number of bins before the current one considered for aggregation., OPTIONAL) INT
aba Aggregation: bins after (Number of bins after the current one considered for aggregation., OPTIONAL) INT
n Number of classifiers (Use only the first k classifiers for predictions., OPTIONAL) INT
outdir The output directory, defaults to the current working directory (.) STRING

Example

java -jar Catchitt.jar predict c=cls/Classifiers.xml a=dnase/Chromatin_accessibility.tsv.gz m=motif1/Motif_scores.tsv.gz m=motif2/Motif_scores.tsv.gz f=hg19.fa.fai p="chr8,chr21" abb=1 aba=4 n=3 outdir=predict


Standard pipeline

The standard Catchitt pipeline would comprise the following steps

  • for a training cell type, collect ChIP-seq peak files (preferably conservative and relaxed peaks) in narrowPeak format and derive labels for genomic regions (Derive labels)
  • for the same cell type, collect chromatin accessibility data (DNase-seq or ATAC-seq) as fold-enrichment tracks or mapping files, and derive chromatin accessibility features from those data (Chromatin accessibility)
  • collect or learn (e.g., using Dimont a set of motif models for the transcription factor of interest, and scan the genome using these motif models (Motif scores)
  • perform iterative training given the labels and feature files (Iterative Training)
  • predict binding probabilities of genomic regions in the same cell type or in other cell types. In the latter case, additional chromatin accessibility data for these target cell types need to be collected and features need to be derived as in step 2. (Prediction)


Version history

  • Catchitt v0.1: Initial release
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