Hi Is it possible to trim a variable number of a specific nucleotide from the 3' ends of fastq RNA reads? The "Manipulate Fastq" utility in Galaxy may have this ability but I do not know how to create a custom inquiry. Thanks in advance for any assistance. Larry
You could use the adaptor clip with e.g. a custom poly-A 'adaptor' its in FASTX-Toolkit for FASTQ data best, ido On Jul 28, 2013, at 8:44 PM, Larry Simpson <larrys3255@gmail.com> wrote:
Hi
Is it possible to trim a variable number of a specific nucleotide from the 3' ends of fastq RNA reads? The "Manipulate Fastq" utility in Galaxy may have this ability but I do not know how to create a custom inquiry.
Thanks in advance for any assistance.
Larry
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Hello Larry, The "Manipulate Fastq" tool only brings up the regular trimmer tools again once "sequence and trim" are selected, so this will not work. And a regular expression could be used as a filter, but that will not actually trim the data. If you choose to filter, this regular expression would find sequences with variable length poly-G at the end. This one actually finds "one or more", so not really poly - this is for you to modify. Change the number in the {} to make a minimum required length. ^.*[A|T|C|N]G{1}G*$ Are you trying to trim poly-A? If using a local instance, repeat masker was just added to the Tool Shed and could be quicker. But if using the public Main server, the adapter clip idea from Ido is very good - certainly worth a try. The other option is to just go ahead and align the data. If the region is long for all sequences, or some subset (you could pull out those that are very long), then do a blanket end length trim on all, put back together any files you have split apart, and let the aligner deal with the remaining trailing bases. "Manipulate Fastq" can be used to subset the file - just run it twice (or as many times as needed to get all the data uniquely into distinct files to merge later. Best, Jen Galaxy team On 7/28/13 11:44 AM, Larry Simpson wrote:
Hi
Is it possible to trim a variable number of a specific nucleotide from the 3' ends of fastq RNA reads? The "Manipulate Fastq" utility in Galaxy may have this ability but I do not know how to create a custom inquiry.
Thanks in advance for any assistance.
Larry
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
To search Galaxy mailing lists use the unified search at:
-- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org
participants (3)
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Ido Tamir -
Jennifer Jackson -
Larry Simpson