## How to generate restriction fragment files ?

Digest the reference genome by the provided restriction enzymes(s) and generate a BED file with the list of restriction fragments after digestion. This file can then be used by HiC-Pro (GENOME_FRAGMENT) for the data processing. Note that the cutting site of the restriction enzyme has to be specified using the '^' character. The restriction enzymes HindIII, DpnII and BglII are encoded within the script and are therefore recognized if specified to the program. Finally, multiple restriction enzymes can also be provided.

## Digest the mm9 genome by HindIII
   HICPRO_PATH/bin/utils/digest_genome.py -r A^AGCTT -o mm9_hindiii.bed mm9.fasta

## The same ...
   HICPRO_PATH/bin/utils/digest_genome.py -r hindiii -o mm9_hindiii.bed mm9.fasta

## Double digestion, HindIII + DpnII
   HICPRO_PATH/bin/utils/digest_genome.py -r hindiii dpnii -o mm9_hindiii_dpnii.bed mm9.fasta

## How to generate chromosome size files ?

The chromosome size files can be easily find on the UCSC genome browser. Otherwise, they can also be generated using other tools such R.

require(BSgenome.Hsapiens.UCSC.hg19)

human_chr <- seqlevels(BSgenome.Hsapiens.UCSC.hg19)[1:25] chrom.size <- seqlengths(BSgenome.Hsapiens.UCSC.hg19)[human_chr] write.table(chrom_size, file="chrom_hg19.sizes", quote=FALSE, col.names=FALSE, sep="t")