HPTAD is a method for calling topologically associating domains (TADs) from HiChIP or PLAC-seq datasets.
Two of the required inputs for HPTAD can be generated using MAPS (detailed in this paper). This preprocessing pipeline, called feather, converts aligned, sorted, and merged paired-end reads to long-range and short-range .bed/.bedpe files. For questions regarding HPTAD please email Ming Hu (hum@ccf.org) or Yun Li (yunli@med.unc.edu).
The requirements and details for running this software are provided below:
The HPTAD R program was tested and run on Linux and requires several readily available packages. We list the versions used in testing and development with the caveat that (slightly) older and newer versions should work, but caveat utilitor.
R 3.6.0
chr10 22142530 22142880
chr10 22142830 22143070
chr10 35110060 35110270
chr10 58223870 58224100
chr11 39148660 39148860
Running the script HPTAD.R involves supplying arguments via the command line, most indicating the location of the inputs listed above.
The files required to run HPTAD on an example dataset are provided in the example folder. Sample command line submission:
Rscript HPTAD.R \
-i example \
-o test \
-p foo \
-C example/ChIP/foo.narrowPeak \
-c 19 \
-f example/features/foo_F_GC_M_MboI_40Kb_el.txt \
-x example/filter/foo_filterlist.bed \
-b 40000
Output is provided as a tab separated value files containing chromosome, start, and end position of TAD regions for each chromosome analyzed.