I am trying to analyze my .fastq files (MiSeq exon reads) with the jMHC software, but output files I have obtained have no results.
I think I might be doing something wrong during the first step: "connect to database". Because on the "import/extracting" step, I open all my .fastq files, click "Start", and it shows this message:
"Success! Processed: 139, Imported: 0".
So I assume it is reading the files OK, but not importing them to the "database"? Could it be the extension of my files? The software says it operates on FASTA files. Are .fastq files not compatible?
Anybody that has successfully run this program could give me a hand?