Hello Matthew,

Lucinda is correct, this tool does not interpret the new ID format correctly. I have opened a bitbucket ticket to track the issue:
https://bitbucket.org/galaxy/galaxy-central/issue/677/update-joiner-tool-to-work-with-casava-18

For now, there is a work-around:

1 - Make certain to run the FASTQ Groomer with input quality scores set to "Sanger" and leave the rest of the form options as default.

2 - Use the tool "NGS: QC and manipulation -> FASTX-Toolkit for FASTQ data -> Rename sequences" to set the sequence names as "numeric".

Do #1 & #2 for each file.

3 - Run Joiner with the file orders as appropriate for left/right.

Thanks for reporting the issue!

Best,

Jen
Galaxy team

On 11/8/11 11:19 AM, Matthew Herron wrote:
Hi,
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 4emptyformat: 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). I have tried this with
Sanger and with Illumina 1.3+ quality scores, and in both (left-right)
orientations. I've pasted the beginnings of the two files below my
signature in case this is useful for diagnosing the problem.
Can anyone tell me what I'm doing wrong?  Thanks,

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