hicAggregateContacts (version 3.7.5+galaxy0)

Matrix to compute on:

Interactions between regions in this BED file are plotted:

Interactions between regions in first and second BED file are plotted:

Minimum range to consider interactions:

The minimum range should be farer from the diagonal than median TAD size in order to reduce background interactions.

Maximum range to consider interactions:

Regions to consider.:

Row wise:

If given,the insteractions between each row of the BED file and its corresponding row of the BED2 file are computed. If intra-chromosomal contacts are computed, the rows with different chromosomes are ignored. If inter-chromosomal, the rows with same chromosomes are ignored. It keeps all the rows if `all`.

Per chromosome:

If set, it generates a plot per chromosome. It is only affected if intra-chromosomal contacts are of interest.

List of chromosomes to plots

List of chromosomes to plot 0

Number of bins to include in the submatrix:

The bed regions will be centered between -half number of bins and +half number of bins indicated.

Type of transformation for the matrix:

If total counts are selected, then the sub-matrix values are divided by the total counts for normalization. If z-score or obs/exp are selected, then H-C matrix is converted into a z-score or observed / expected matrix.

Type of operation to compute final matrix:

Consider strand direction:

This parameter specifies if the strand information is taken into account for the aggregation. It has the effect that the contacts of a reverse strand region are inverted e.g. [1,2,3] becomes [3,2,1].

Large regions operation:

If a given coordinate in the bed file is larger than a bin of the input matrix, by default only the first bin is taken into account. However there are more posibilities to handel such a case. Users can ask for the last bin or for center of the region. As an example if a region falls into bins [4,5,6] and `--numberOfBins = 2` then if first, bins [3,4,5] are kept. If last: [5,6,7] and if center: [4,5,6].

Number of clusters per chromosome:

When this option is set, then the matrix is split into clusters using the hierarchical clustering algorithm, using 'ward linkage'. hclust could be very slow if you have >1000 submatrices per chromosome. In those cases, you might prefer kmeans.

How to cluster:

Options are 'full', 'center' and 'diagonal'. The full clustering ' 'takes all values of each submatrix for clustering. center, takes only a square of ' 'length 3x3 from each submatrix and uses only this values for clustering. With the ' 'diagonal option the clustering is only carried out based on the submatrix diagonal ' '(representing values at the same distance to each other)

Plot type:

Color map to use for the heatmap:

Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html

vMin:

Minimum value of the plotted score.

vMax:

Maximum value of the plotted score.

Image output format:

Optional output files:

Aggregation of Hi-C contacts

hicAggregateContacts allows plotting of aggregated Hi-C sub-matrices of a specified list of positions. Positions of interest can for example be binding sites of a specific protein that were determined by ChIP-seq or genetic elements as transcription start sites of active genes.

Usage

This tool must be used on Hi-C matrices corrected by hicCorrectMatrix. One should also consider bigger bins than restriction enzyme resolution bins using hicMergeMatrixBins.

Optional parameters

Optional data output can be selected:

Save values underlying the final matrix: if this option is given, then the values underlying the final matrix will be saved to tab-delimited tables (one per chromosome) using the indicated prefix, for example TSS_to_TSS_chrX.tab. If clustering is performed, then the values are saved including the cluster_id a in TSS_to_TSS_chrX_cluster_1.tab

Save the position of the contacts: if this option is given, then the position of the contacts is saved as (chrom1, start1, end1, chrom2, start2, end2) where chrom_n, start_n, end_n correspond to the pair of positions used to compute the submatrix. The data is saved per chromosome and per cluster separately (one file each).

Heatmap file per chromosome: if given, a heatmap file (per chromosome) is saved. Each row in the heatmap contains the diagonal of each of the submatrices centered on the bed file. This file is useful to get an idea of the values that are used for the aggregate matrix and to determine the fraction of submatrices that are aggregated that may have an enrichment at the center.

Output

hicAggregateContacts outputs a plot of aggregated contacts.

Below, you can find an example of an aggregate Hi-C matrix obtained from Drosophila melanogaster Hi-C data. The interactions are plotted at binding sites of a protein that were determined by ChIP-seq. We plot sub-matrices of 30 bins (1.5 kb bin size, 45 kb in total). The regions specified in the BED file will be centered between half number of bins and the other half number of bins.The considered range is 300-1000 kb. The range should be adjusted and only contain contacts larger than TAD size to reduce background interactions.

/repository/static/images/2744bf450c16ed98/hicAggregateContacts.png

This example was calculated using mean interactions of an observed vs. expected transformed Hi-C matrix. Additional options for the matrix transformation are total-counts or z-score. Aggregate contacts can be plotted in 2D or 3D.

For more information about HiCExplorer please consider our documentation on readthedocs.io