Debular trim length

[Hasinika (Hasinika Gamage)]

Hi,

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.

Cheers
Hasinika

[thermokarst]

That sounds like a good start, @Hasinika. How about you try to experiment with a few different settings to try to understand what the impact is on the resulting data? That's a great way to get familiar with things. Keep us posted! :qiime2:

[Hasinika (Hasinika Gamage)]

Thanks for the reply @thermokarst Sorry if I was not clear, my question was do I set the trim length based on just the reverse read? and trim both the forward and reverse reads at ~140 in this case?

Thank you.

[thermokarst]

Hi @Hasinika - that's up to you, I encourage you to try it a few different ways and let us know how it goes.