ERROR: Missing hic_results or bowtie_results files for B651rep1; either exclude the sample or manage the file architecture/input #98
Description
ERROR: Missing hic_results or bowtie_results files for B651rep1; either exclude the sample or manage the file architecture/input
I run into this error when I submit my script for hichipper. I saw a similar issue before and the problem there was that the user had not run step2 of HiC-Pro. I have run step2 of HiC-Pro and have an ".allValidPairs" file. This is my first time running both HiC-Pro/hichipper with HiChIP data that was produced using MNase rather than a restriction enzyme and I'm wondering if that's why I'm running into this issue. I will also note that I don't have a bwt2_local folder in my HiC-Pro output and I don't have ".bwt2pairs.DEPairs", ".REPairs", or ".SCPairs" in my hic_results folder either (I'm assuming this is because I didn't use a RE for the assay.