D:\Illumina\MiSeqOutputor on a network path that you specify. After on-instrument secondary analysis is complete, the reads are available in
*.fastq.gzfiles in the subfolder
/Data/Intensities/BaseCalls/of the run folder. For example, the first file may be called
*.fastq.gzfiles from your Ion Torrent PGM instrument, follow the instructions in How do I upload my data files?.
.SFFfile as input. The applet expects the reads to be gzip compressed (
*.sff.gz) and will produce a SAM file as output.
schannel: failed to setup extended errorswhen running the Upload Agent on Windows. What can I do?