:point_down: HiCorr on Arima

• Download the code from this repository, "bin/Arima/"
  
• Download the reference files for Arima (mm10/hg19 genome build)

wget --no-check-certificate https://hiview10.gene.cwru.edu/public/DeepLoop_ref/ref/Arima_HiCorr_ref.tar.gz
# old path: http://hiview.case.edu/ssz20/tmp.HiCorr.ref/ref/Arima_HiCorr_ref.tar.gz
tar -xvf Arima_HiCorr_ref.tar.gz

• Check the preprocessing for Arima data (mapping, fragments filter, outs are cis and trans fragment loops)
  
• One example log for preprocessing two biological reps of Arima Hi-C
• Run HiCorr on Arima data:

bash HiCorr_Arima.sh Arima_HiCorr_ref/ bin/Arima/ <frag_loop.name.cis> <frag_loop.name.trans> <name> <hg19/mm10>
   # specify the path of downloaded unzipped reference file and scripts
   # input two fragment loop files genrated from preprocessing step
   # specifiy outputname prefix
   # specify genome build, the provided reference only include hg19 and mm10