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 On Apr 4, 2010, at 10:32 PM, Florent Angly 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 _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user