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Old 04-16-2014, 04:26 PM   #2
mbzmg1
Junior Member
 
Location: Colorado

Join Date: Feb 2012
Posts: 9
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The default output format for Ion Torrent is .bam (even if not mapping the reads).

You need to fill out the settings for the FileExporter plugin before it will generate the .fastq files correctly.

You will find the .bam files at:
/results/analysis/output/Home/NAME_OF_RUN/

and the .fastq files at:
/results/analysis/output/Home/NAME_OF_RUN/plugin_out/downloads/

(this is for the current version of TSS and may change with updates)

Hope this helps.
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