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Question: How To Turn On Debug?
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gravatar for Peter Andrews
8.7 years ago by
Peter Andrews • 30
Peter Andrews • 30 wrote:
I received a server error and would like to more detailed information Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) How do I 'turn debug on'?. I am using the public galaxy instance http://main.g2.bx.psu.edu/ Thanks, Peter Andrews -- Peter Andrews Programmer Computational Genetics Lab Dartmouth Hitchcock Medical Center (603) 653-9963
galaxy • 1.4k views
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modified 8.7 years ago by Florent Angly • 370 • written 8.7 years ago by Peter Andrews • 30
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gravatar for Florent Angly
8.7 years ago by
Florent Angly • 370
Florent Angly • 370 wrote:
Hi list, Is there a tool in Galaxy to trim the end of FASTQ reads based on their quality, say to remove all base pairs at the end of a read that have a quality smaller than 20? I know about the tool that trims an arbitrary number of base pairs at the end of reads and the filter tool that can filter out sequences that have some base pairs with a quality value below some threshold but they are different from what I need. Regards, Florent
ADD COMMENT • link written 8.7 years ago by Florent Angly • 370
Hi Florent, You are correct that there is not currently a tool to trim directly by quality in Galaxy; currently the the Summary statistics and boxplot tools are used to determine good cut off for use in the trim by column tool; percentage of read length can be more useful on variable length reads. However, adding a tool that can directly trim reads based upon a threshold quality score seems like a natural fit for Galaxy, when uniform read length is not present at the start and/or not a requirement at the end and the percentage-of-read-length method is not sufficient. Lets verify that you are looking for something like this, where 'x' is a low quality base and 'o' is a high quality base: Start with: xxxooooxxooooxxx after trimming ends for 'x': ooooxxoooo So that trimming happens only from the ends and stops as soon as a base above the threshold is found and internal low quality bases are not considered. Thanks, Dan
ADD REPLY • link written 8.7 years ago by Daniel Blankenberg ♦♦ 1.7k
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