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5.3 years ago by

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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modified 5.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 5.3 years ago by Larry Simpson • 30

5.3 years ago by

Ido M. Tamir • 280

Austria

Ido M. Tamir • 280 wrote:

You could use the adaptor clip with e.g. a custom poly-A 'adaptor' its in FASTX-Toolkit for FASTQ data best, ido

ADD COMMENT • link written 5.3 years ago by Ido M. Tamir • 280

5.3 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

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 -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

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