What am I doing wrong? My files have an extension of .fastq. I am told that these files contain raw data from an Illumina MiSeq sequencer. Therefore, I mark these files as fastqillumina. I am getting an error message. I have tried several times with no success.
I have tried with some success to load these files with the auto-detect but I am not sure if my files will align properly if I don't identify them as fastqillumina. All my research tells me that I must identify my files properly.
Can you help me?