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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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there is a tool called filter FASTQ (Filter FASTQ reads by quality score and length) under GENERIC FASTQ MANIPULATION -
Galaxy filter quality help
Hello,
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
geneartComment
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filterQC
Before using Filter FastQ you must use the FASTQ Groomer.Comment
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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