After creating the custom primer file, I ran this module and all my fastq files were empty. Please bear in mind that this dataset was produced on an Iontorrent platform but it should in theory be in a Illumnia data format. See the following pipe:
/nobackup/afodor_research/blj_pipeline/jjohn443/2015_EoE_Demultiplex_2020Jun30/
After creating the custom primer file, I ran this module and all my fastq files were empty. Please bear in mind that this dataset was produced on an Iontorrent platform but it should in theory be in a Illumnia data format. See the following pipe: /nobackup/afodor_research/blj_pipeline/jjohn443/2015_EoE_Demultiplex_2020Jun30/