Question: Problem with FASTQ Quality trimmer by sliding window
gravatar for mauricio.galvan
4.5 years ago by
mauricio.galvan0 wrote:

Hi, I´m using the FASTQ Quality trimmer by sliding window with a quality score of 25, and after running the FASTQC: Read QC report I still getting sequence quality lower than 25, is this possible? am I doing something wrong here?

galaxy • 2.7k views
ADD COMMENTlink modified 4.2 years ago by Leontovich, Alexey A., Ph.D.30 • written 4.5 years ago by mauricio.galvan0
gravatar for Wolfgang Maier
4.5 years ago by
Wolfgang Maier600 wrote:


this is taken from the tool's help:


This tool allows you to trim the ends of reads based upon the aggregate value of quality scores found within a sliding window; a sliding window of size 1 is equivalent to 'simple' trimming of the ends.

The user specifies the aggregating action (min, max, sum, mean) to perform on the quality score values found within the sliding window to be used with the user defined comparison operation and comparison value.


What it says is that unless you're using a window size of 1, what you observe is entirely possible.

If, for example, you set a window size of 5 and the aggregating action to mean, the tool will trim each read when the mean quality score over any consecutive 5 bases drops below 25, which is obviously different from trimming at the first score < 25.


ADD COMMENTlink written 4.5 years ago by Wolfgang Maier600
gravatar for Leontovich, Alexey A., Ph.D.
4.2 years ago by
United States

It seems that this trimming tool is not doing anything. I spent days experimenting with different options: Window size, number of bases to exclude, aggregate function (action), Quality score cut-off.... I get the same box and whiskers plot using FASTQC tool.


ADD COMMENTlink written 4.2 years ago by Leontovich, Alexey A., Ph.D.30
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