Quick start

(Assuming user has already installed the prerequisites, and is using the FitHiChIP source downloaded from GitHub)

The file sample_script.sh (provided in GitHub archive) contains the sample script to execute FitHiChIP. The sample command to run FitHiChIP is:

bash FitHiChIP_HiCPro.sh -C configuration_file_name

where,

FitHiChIP_HiCPro.sh: main executable of FitHiChIP pipeline.

In the GitHub archive, four configuration files are provided for users to check:

  1. configfile_BiasCorrection_CoverageBias:

    • This configuration file can be used as template to execute FitHiChIP(L) & FitHiChIP(L+M) with coverage bias regression.

  2. configfile_BiasCorrection_ICEBias:

    • Template of configuration file corresponding to FitHiChIP(L) & FitHiChIP(L+M) with ICE bias regression.

  3. configfile_P2P_BiasCorrection_CoverageBias:

    • Template of configuration file corresponding to FitHiChIP(S) & FitHiChIP(S+M) with coverage bias regression.

  4. configfile_P2P_BiasCorrection_ICEBias:

    • Template of configuration file corresponding to FitHiChIP(S) & FitHiChIP(S+M) with ICE bias regression.

Note

  • Selection of the configuration file depends on the FitHiChIP background model (i.e. loose L or stringent S) and the bias regression method (i.e. coverage bias or ICE bias) to be used.

  • User should tally these configuration files with the parameters mentioned in section Setting up configuration file for understanding the configuration parameters.

  • For installing FitHiChIP via Docker or Singularity image, please check the section Installation

Description of the test data

Above mentioned configuration files are set according to the dataset provided in the folder TestData within the GitHub archieve. The folder contains sample HiChIP data, peak files, and also sample dataset for differential analysis of HiChIP loops.

User need to download following files within the "TestData" folder for executing FitHiChIP:

  1. Sample_ValidPairs.txt.gz:

    Sample valid pairs file, an output from HiC-Pro pipeline.

  2. Sample.Peaks.gz:

    Reference ChIP-seq peak information correspondin to the given data.

  3. chrom_hg19.sizes:

    Size of individual chromosomes corresponding to the reference genome hg19

    Note

    For different reference genome, user needs to download appropriate chromosome size file from the UCSC genome browser site.

    For example, above mentioned file can be downloaded from the link: <http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.chrom.sizes>

Note

The folder "TestData" also contains one directory "DiffLoopData" which contains dataset regarding differential HiChIP loop analysis. The dataset is described in the page Differential analysis of HiChIP loops.

Configuration parameters according to the test data

Please check the page Setting up configuration file for a detailed description.

Sample logs from the console, corresponding to the TestData

Upon executing the test data with one of the above mentioned configuration files, user can tally the output logs in console with the model console output provided in the file SampleConsoleOutput.txt, to debug about any errors regarding installation / execution.

Output file description

Output files are generated within the specified OutDir.

User can check the details of FitHiChIP output files are provided in the page Details of FitHiChIP outputs.

In particular, user should check for the following files:

  1. PREFIX.interactions_FitHiC_Q"QVALUE".bed

  2. PREFIX.interactions_FitHiC_Q"QVALUE"_MergeNearContacts.bed (generated only if MergeInt = 1)