I'm really interested in applying HiCorr/DeepLoop to my HiC data set as they are low-input HiC samples. I have used the Arima 4-enzyme low input kit and processed my fastq files using HiC-Pro. Using the workflow, I've converted the validpairs.gz file using validPairs_2_fragloop.md with the mm10.Arima.frag.bed file. When I use HiCorr, I get anchor_2_anchor files for each chromosome, but the expected and observed values are both 0 for each loop. I have attached my output error below:
hicorrOutputError.txt
Do you have any suggestions of where I might be going wrong?
Input:
hicorr.txt
I'm really interested in applying HiCorr/DeepLoop to my HiC data set as they are low-input HiC samples. I have used the Arima 4-enzyme low input kit and processed my fastq files using HiC-Pro. Using the workflow, I've converted the validpairs.gz file using validPairs_2_fragloop.md with the mm10.Arima.frag.bed file. When I use HiCorr, I get anchor_2_anchor files for each chromosome, but the expected and observed values are both 0 for each loop. I have attached my output error below:
hicorrOutputError.txt
Do you have any suggestions of where I might be going wrong?
Input:
hicorr.txt