DADA2 Truncating Reverse Read

[ninaxhua (Nina Hua)]

Hello,

I was wondering if it was concerning to see this message occur multiple times during error learning and denoising steps: "Not all sequences were the same length." This occurred when I used '0' as --p-trunc-len-r value since I didn't want to truncate the reverse read.

However, when I re-ran DADA2 with --p-trunc-len-r value set to the last sequence base position of the reverse read in the Demux visualization, I didn't encounter the message. Essentially, I did not truncate the reverse read right?

[thermokarst]

Hey there @ninaxhua!

@ninaxhua

I used ‘0’ as --p-trunc-len-r value since I didn’t want to truncate the reverse read.

@ninaxhua

Essentially, I did not truncate the reverse read right?

No, I don't think that is right - I think you did truncate your sequences. The demux summarize method only uses a subsample of reads by default (10000 reads), which means that you could actually have longer reads that just aren't represented in the viz. You could rerun and specify the --p-n parameter to whatever the total number of reads are to get a more complete picture.

Hope that helps! :qiime2: