FitHiChIP requests different input than specified in documentation #104
Description
Hello,
when running FitHiChIP via docker with the following command:
bash ./FitHiChIP_Docker.sh -C /path/to/fithichip_config
I eventually receive this:
================ Verifying input configuration parameters =================
There are three ways to provide FitHiChIP input:
- provide valid pairs file (from HiC pro pipeline),
- Provide both bin interval and matrix files (from HiC pro pipeline), or
- provide a set of locus pairs along with their contact counts (7 columns).
But user did not provide any of these input configurations. - exit !!
even though the documentation says that an .mcool file can be used as input.
This is how my config file looks:
COOL="/path/to/sertoli.mcool"
PeakFile="/path/to/file.bed"
OutDir="/path/to/fithichip_results"
ChrSizeFile="/path/to/mm10.chrom.sizes"
BINSIZE=5000
QVALUE=0.01
UseP2PBackgrnd=0
MergeInt=1
PREFIX="fitHiChIP_5k"
OverWrite=1
What am I missing here?
Thanks!