I am performing de novo transcriptome assembly. I have used Trimmomatic to quality filter my reads. I used the argument: SLIDINGWINDOW:4:30 Can someone explain what this means?
My understanding is that the sliding window approach will cut the read when the average quality of each 4-nt window falls below a quality score of 30.
I guess I am getting confused on the "cut the read" part. If someone could clarify this, it would be much appreciated! Also, is the quality score of 30 a phred score?
Thanks for the help! Nikelle