Question: Question
gravatar for Larry Simpson
5.3 years ago by
Larry Simpson30 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
galaxy • 801 views
ADD COMMENTlink modified 5.3 years ago by Jennifer Hillman Jackson25k • written 5.3 years ago by Larry Simpson30
gravatar for Ido M. Tamir
5.3 years ago by
Ido M. Tamir280
Ido M. Tamir280 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 COMMENTlink written 5.3 years ago by Ido M. Tamir280
gravatar for Jennifer Hillman Jackson
5.3 years ago by
United States
Jennifer Hillman Jackson25k 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
ADD COMMENTlink written 5.3 years ago by Jennifer Hillman Jackson25k
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