Hi Matthew, Are you by chance using sequences with the newer CASAVA 1.8+ formatting? For example: @HWI-ST765:83:D091AACXX:1:1101:1202:2130 If so, this tool is known to not work correctly (it skips over the IDs). We do consider it a priority to update the tool. You can track our progress by following the bitbucket ticket here: http://bitbucket.org/galaxy/galaxy-central/issue/677/update-joiner-tool-to-w... Thank you for your patience, Jen Galaxy team On 11/3/11 5:45 PM, Matthew Herron wrote:

I am trying to join two groomed fastq files from a paired-end Illumina read using the fastq joiner tool. The drop-down menus correctly identify the groomed fastq files, but after cranking for a few minutes the tool produces empty output: "FASTQ joiner on data 5 and data 4 empty format: fastqsanger, database: ? Info: There were 3497909 known sequence reads not utilized. Joined 0 of 3497909 read pairs (0.00%)." The files have the same number of reads (3497909), reads have the same number of bases (102), and the joiner tool doesn't have any options (other than choosing the two files to join). Can anyone tell me what I'm doing wrong? Thanks,

-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support