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Old 10-01-2012, 02:31 PM   #1
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Location: Iowa

Join Date: Oct 2012
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Default Galaxy tool to filter low mapping quality reads?

Does anybody know if there is a way to remove low quality reads on Galaxy? it could be easily done using command line based bamtools and all I have to do is specify the map quality. Is there an equivalent version on galaxy? Or is there a published workflow that does it for you? Thanks.
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Old 10-02-2012, 08:46 AM   #2
Location: michigan

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there is a tool called filter FASTQ (Filter FASTQ reads by quality score and length) under GENERIC FASTQ MANIPULATION
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Old 10-02-2012, 09:11 AM   #3
Location: DC area

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Default Galaxy filter quality help

trying to use galaxy to perform NGS analysis.
I have created a history that contains my datasets. Now when I go down to pull the filterQC application I dont see my datasets in the "library to filter". How do I pull my datasets into the stream?
Tutorial shows how to get data from UCSC and also if I have a work flow created then I can do it, but without a workflow , if I have to just use one tool to do the job how do I get my datasets to show up for an operation?
Thanks for ur time
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Old 08-08-2013, 06:56 AM   #4
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Default filterQC

Before using Filter FastQ you must use the FASTQ Groomer.
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