HPTAD user manual

What is HPTAD?

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

• argparse 2.0.3
• data.table 1.14.2
• dplyr 1.0.7
• MASS 7.3.51.4
• VGAM 1.1.3
• zoo 1.8.5

Inputs

1. .long.intra.bedpe file: obtained from MAPS as referenced above
2. .shrt.vip.bed file: obtained from MAPS as referenced above
3. Genomic features file: can be downloaded from Genomic features
4. 1-D ChIP peaks: can be obtained by running MACS2 on corresponding ChIP-seq data, or on short-range reads
5. Filter file (optional):
   • This is used if you want to exclude genomic regions from MAPS analysis. Reads mapping to those regions will be ignored. Set to “None” if not filtering any regions. A filter file is a tab delimited table containing three columns (no header) representing chromosome, the start position, and end position of any loci you wish to exclude.

     chr10   22142530 22142880
     chr10   22142830 22143070
     chr10   35110060 35110270
     chr10   58223870 58224100
     chr11   39148660 39148860

Usage

Running the script HPTAD.R involves supplying arguments via the command line, most indicating the location of the inputs listed above.

• -i, --indir: directory containing both long-range and short-range .bed/.bedpe files for desired chromosomes (required)
• -o, --outdir: directory where output is to be written (required)
• -p, --prefix: name of dataset: should be identical to prefix of .bed/.bedpe files (required)
• -C, --chip: full path to ChIP peak file (required)
• -c, --chromosomes: comma separated list of chromosomes to be analyzed (1,2,3 e.g.) (required)
• -f, --features: full path to features file (required)
• -x, --filter: full path to filter file, or 'None' (optional: default = 'None')
• -b, --binsize: bin size for analysis in base pair length (required)
• -u, --upperlimit: upper limit of distance between bins to be analyzed (optional: default = 2Mb)

Example

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.