On Fri, Jul 6, 2012 at 3:07 AM, Aarti Desai <aarti_desai@persistent.co.in> wrote:

These show up in the history with the appropriate size. But when I choose the “Map with BWA for Illumina” option, the two fastq files do not show up in the FASTQ file drop down.

Hi Aarti, Most tools in galaxy that work with fastq file need specifically fastqsanger input file. Even if your file have the quality values in Sanger format, the auto detect format logic won't be able to determine this. If you know you fastq file are in fact in Sanger format, editing your file metadata and selecting fastqsanger for the format would do the trick. If you aren't sure, you should use Fastq Groomer tool to convert them to Sanger format. I would recommend to watch the several screencast describing mapping analysis in Galaxy. Hope it helps, Carlos