FitHiChIP

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Differential loop analysis

1

Hello, I'm trying to run differential loop analysis using the script Imp_Scripts/DiffAnalysisHiChIP.r on a 2-conditions but only 1 replicate per condition data, without ChIP bam files. However I got 0...

helenhuangmath

An easy way to get the whole genome expected interaction matrix

1

FitHiChIP is an explicit and clearly written normalization method for HiChIP data processing. Beyond significant loop calling, I want to develop a genome-wide background model by using FitHiChIP-produced bias, regression...

zhangylab

Error in .compressOffsets(y, offset = offset) : offsets must be finite values Calls: ApplyEdgeR -> exactTest -> mglmOneGroup -> .compressOffsets

1

Hi, I'm doing the differential loops analysis by `Imp_Scripts/DiffAnalysisHiChIP.r` And It went error after I just switched the positions of the input files in my execution script. ```{shell} Rscript Imp_Scripts/DiffAnalysisHiChIP.r...

Gemma-Zhang-326

FitHiChIP requests different input than specified in documentation

1

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...

roniweiss12

Fix sorting with header row;

1

Solution is to use a subshell to combine the outputs of a head and tail | sort

moritzschaefer

run 2to3 (only changes one import and adds '()' to a lot of print statements

1

Fixes a part of #54

moritzschaefer

The file containing ChIP coverage data does not include the label information, only the coverage values, when trying to append the label it just copies the last column and as...

armenabnousi

How to get common loops between two samples

4

Hello, I have a question regarding categorization of loops. So I have used FithiChIP for callong loops for two samples of CTCF-HiChIPs (L, peak to all, FDR 0.01) and I...

remeseirogrp

option to fragment interactions?

1

Hi, I'm curious if it is possible to adapt FitHiChIP method for obtaining fragment interactions rather than binsize interactions, since the specific bin size would usually be smaller or larger...

hugch2020

Lower number of Significant Interactions

1

Hi, First thank you for providing excellent documentation on FitHiChIP! I am running FitHiChIP on my HiChIP data generated from HiCPro (.allValidPairs). I am using the following parameters. ``` IntType...

koushik20