HI I have a question, when I use SLIDINGWINDOW option in trimmomatic, what does exact mean for the windownsize, like SLIDINGWINDOW:4:15, what is 4 mean? I am more familiar with fastx-toolkit, that use percent like 75 mean %75 base must be over the quality like 20. Does this number 4 in slidingwindow has the same function?
Thank you
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Tonyzeng •
I take it you didn't read the manual. Had you done so, you would have found the following:
Perform a sliding window trimming, cutting once the average quality within the window falls below a threshold. By considering multiple bases, a single poor quality base will not cause the removal of high quality data later in the read.
SLIDINGWINDOW:<windowSize>:<requiredQuality>
thank you, dpryan79, does my understanding right for the above? 80:20 mean cut off any reads that have 80bases below the 20 quality score?
Not exactly. It averages the quality scores of the 80 bases. If that average is below 20, then it trims. If you had 79 bases with scores of 19 and 1 base with a score of 110 (not that that would ever occur), then the window wouldn't be trimmed. There's no exact equivalent with slidingwindow in trimmomatic to what you used in fastx-toolkit.
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suppose my reads have 100bp length, if I want to filter these reads with 80% bases under 20 quality, should I use Slidiningwindow as 80:20, does my understanding right?