I am trying to use a FASTQ file of RNA-Seq results from an Ion Proton Sequencer. The FASTQ file seems to have uploaded fine, but it doesn't show up in the "FASTQ" file list for Tophat2 and other programs. I read about the FASTQ groomer and tried running that using the "Sanger&Illumina" option but got an error message which I could only read part of. Should I have chosen one of the other platform options or is there some other way to convert the data so that I can use the data in Galaxy?
Any help would be appreciated!