Processing the Test Dataset

To confirm HiCUP functions correctly on your system please download the Test Hi-C dataset. The test files ‘test_dataset1.fastq’ and ‘test_dataset2.fastq’ both contain human Hi-C reads in Sanger FASTQ format.

1) Extract the tar archive before processing:

tar -xvzf hicup_v0.X.Y.tar.gz

2) If necessary, create Bowtie/Bowtie indices of the Homo sapiens GRCh37 genome (chromosomes 1,…,22, X, Y and MT).

Example commands:

bowtie-build 1.fa,2.fa,...,MT.fa human_GRCh37

bowtie2-build 1.fa,2.fa,...,MT.fa human_GRCh37

3) Using HiCUP Digester create a reference genome of Homo sapiens GRCh37 all chromosomes (1,…,22, X, Y and MT) digested with HindIII (A^AGCTT).

Example command:

hicup_digester --genome Human_GRCh37 --re1 A^AGCTT,HindIII *.fa

4) Edit a copy of the hicup.conf configuration file so it has the following parameters:

Zip: 1
Keep: 0
Threads: 1
Bowtie: [Path to Bowtie on your system, if using this aligner]
Bowtie2: Path to Bowtie2 on your system, if using this aligner]
Digest: [Path to digest file on your system]
Index: [Path to Bowtie/Bowtie2 indices on your system]
R: [Path to R on your system]
Format: phred33-quals
Shortest: 150
Longest: 800

5) Run the pipeline:

Execute HiCUP with the command:

hicup --config [Configuration Filename]