Closed YiweiNiu closed 1 year ago
Hi Yiwei,
The bias file is the output of a normalization method for HI-C data that contains the bias factors for each bin. See "FitHiC2 bias file format" here for more: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7451401/
Fit-Hi-C has an implementation of the K-R algorithm for normalization out of the box; you can use this to generate the bias files: https://github.com/ay-lab/fithic/blob/master/fithic/utils/HiCKRy.py
Thanks for your quick reply.
I still have one question, how do I supply the bias files to dcHiC
?
I mean, I do not find an command line option to specify the bias file in the fithic
step of dchicf.r
.
See the error output -- you should run these biases and put them in a director 'biases' in the directory that you are running dcHiC
Please generate the bias files for each sample provided in the input.txt file
Create an additional folder 'biases' under current path and dump all the *.biases.gz files inside it
You should create these with the same prefixes specified in input.txt
, as the fithic step inside dcHiC looks for bias files using those prefixes: bias<- normalizePath(paste0("biases/",prefix,".biases.gz"))
Let me know if this helps / if any other issues arise!
Thanks for your reply. Maybe you could modify the readme.md
to add this.
Hi,
Thanks for developing this useful tool.
When running the step of
fithic
, I got the following error.I wonder how to specify the bias files for fithic.
Bests, Yiwei