Differential intra TAD activity (test set)

Instructions

Run the pipeline using a test data set from Mayilaadumveettil et al., 2020.

a) Download the test data manually from https://bit.ly/domainsDiffTest or:

wget https://bit.ly/domainsDiffTest

b) Decompress the test data:

tar xvzf domains-diff-test.tar.gz

c) run the analysis:

cd domains-diff-test

./run.sh PARAMS/params-test.sh

Run the pipeline using custom data.

1. Follow steps a) and b)

2. Create a custom params file in the PARAMS/ directory. You can create a copy of the test params file provided in PARAMS/ (params-test.sh) and then edit the parameters. Edit the 'input variables' and 'annotation parameters' to set the contact matrix, domains directories/files, the matrix resolution and the annotation files. We provide the annotation files for mm10, hg19 and hg38 in DATA/annotation/. We use cpm normalization in the test set but you can also use distance normalization (distnorm).

3. Run the analysis:

./run.sh <CUSTOM-PARAMS-FILE>

Note:

This pipeline requires hic contact matrices in the same format used by HiC-Bench. You can check this format in the test data provided in TEST/matrix-ic/. The matrix files must be named like in 'matrix.chr1.tsv', one file per chromosome.

In the first step this pipeline identifies common tads that are present in both samples according to the criteria specified in the params file. It requires one bed files per sample with the tad coordinates. If you want to focus the analysis on a custom set of tads you must set the <domains1> and <domains2> parameters for the same bed file containing the custom tads. For example, you might want to perform the analysis on all the tads identified in the control/reference sample or separately on the tads identified on each sample.

Output

The pipeline produces results_*.tsv files with the differential tad activity metrics and gene annotation for every TAD. The pipeline generates boxplots, volcano plots and scatter plots.

Test data example:

We use hic data sets from the Mayilaadumveettil et al., 2020 work to compare the tad activity changes in a mESC cell line after depletion of the endogenous CTCF (B.I) (CTCF degron system) against a wild type mESC cell line with normal CTCF activity (B.UI):

Boxplot:

Volcano plot:

Scatter plot:

References

Nishana, M., Ha, C., Rodriguez-Hernaez, J. et al. Defining the relative and combined contribution of CTCF and CTCFL to genomic regulation. Genome Biol 21, 108 (2020). https://doi.org/10.1186/s13059-020-02024-0