I want to extract significant interactions using GOTHiC and I have been going through the literature. It takes mapped reads as input and converts it to GOTHiC readable format. Is there a way that I can obtain this file from the .allvalidPairs or matrix files? If not for these how do I get the .gothic file format from mapped reads of HiC-Pro? Is there any utility available as there is for tools such as juicer?
Also I wanted to know if trimming the reads for adapters is essential for the fastq files I give as input to HiC-Pro. I have been doing that for most of the tools I run the analysis for. Does giving the trimmed reads (for adapter sequences) affect the coverage, since there is trimming involved before alignment in HiC-Pro too?
Hello!
Is it possible to use the HiCPro output files (.allvalidPairs or matrix files) as an input for GOTHiC tool (https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0174744#sec001)
I want to extract significant interactions using GOTHiC and I have been going through the literature. It takes mapped reads as input and converts it to GOTHiC readable format. Is there a way that I can obtain this file from the .allvalidPairs or matrix files? If not for these how do I get the .gothic file format from mapped reads of HiC-Pro? Is there any utility available as there is for tools such as juicer?
Also I wanted to know if trimming the reads for adapters is essential for the fastq files I give as input to HiC-Pro. I have been doing that for most of the tools I run the analysis for. Does giving the trimmed reads (for adapter sequences) affect the coverage, since there is trimming involved before alignment in HiC-Pro too?