Question: Ion Torrent Data Analysis
gravatar for Xu, Jianpeng
5.3 years ago by
Xu, Jianpeng30
Xu, Jianpeng30 wrote:
Hi All, I am trying to use Galaxy to analyze the Ion Torrent data. I have uploaded my data to the galaxy. However, when I try to use FASTQ Quality Trimmer and Trim sequences to trim my fastq files, my file does not show in the FASTQ File menu. Do you know why ? How to fix it? Do these programs work on Ion Torrent data ? Thanks, Jianpeng ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).
galaxy • 2.3k views
ADD COMMENTlink modified 5.3 years ago by Jennifer Hillman Jackson24k • written 5.3 years ago by Xu, Jianpeng30
gravatar for Jennifer Hillman Jackson
5.3 years ago by
United States
Jennifer Hillman Jackson24k wrote:
Hello Jianpeng, The data needs to be assigned to datatype "fastqsanger". This datatype indicates that the quality scores are scaled as Phred+33 (which they most likely are from this technology). The tool "NGS: QC and manipulation -> FASTQGroomer" can be used with the input option "Sanger" for your data to both assign the datatype and perform format verification. Or, optionally, you could just assign the datatype: pencil icon -> Edit datasets -> Datatype tab. If you just assign, and the dataset gives errors with tools, backing up and running the groomer will often tell you exactly where in the file the problem is located (format). Best, Jen Galaxy team -- Jennifer Jackson
ADD COMMENTlink written 5.3 years ago by Jennifer Hillman Jackson24k

I am new to Galaxy and am also having trouble with error messages following an attempted FASTQGroomer run.  I selected "Sanger and Illumina" from the list of "Solexa, Illumina, Sanger & Illumina, Color Space".  I got an error message and it says that the details are "below", but I can't get to the "below" section.

Did I make the wrong selection in the initial FASTQGroomer run or is something else not working?




ADD REPLYlink written 3.7 years ago by avnairn0

Hello, Clicking on the "bug" icon will reveal the detail of the problem. You can ether use the information given to correct your file, or if it is empty, go ahead and complete the the submission of the bug report. I have never seen the latter, but we would be interested in fixing this if it was occurring. 

The problem reported would be based on formatting, not content. To understand more about content and tool options, please see:

Best! Jen, Galaxy team

ADD REPLYlink written 3.7 years ago by Jennifer Hillman Jackson24k
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