I am new to using Debular for denoising and confused about how to determine the --p-trim-length
According to the Moving Pictures tutorial, the length seems to be based on the quality score, it reads "In general, the Deblur developers recommend setting this value to a length where the median quality score begins to drop too low. On these data, the quality plots (prior to quality filtering) suggest a reasonable choice is in the 115 to 130 sequence position range."
I am working with demultiplexed paired-end sequence data (2x250 bp, all reads are 250 bp, not a meta analysis), the forward read is of good quality, whilst the quality of the reverse drops at around 140. In this case, how do I set the trim length?
Thanks for any help in advance.