Cutadapt trimming in ITS tutorial

the_dummy · August 28, 2019, 7:38am

after cutadapt step we have removed adapters and primers. why do we use trim left in dada2 step?
sorry about it if it sounded irrelevent but im new to this

jwdebelius · August 28, 2019, 7:44am

Hi @the_dummy,

Welcome to the forum! I moved your question over to a more general post in user support.

Best,
Justine

Mehrbod_Estaki · August 28, 2019, 9:00am

Hi @the_dummy,
Welcome to the forum and good inquisitive question.

The trim left option in dada2 can be used to either trim adapters (as you have done in vsearch) or remove low quality portions of your reads which sometimes occur during the first 10-20 bp on the 5’ end. This is not uncommon from Illumina runs. When these low quality tails are present, dada2’s internal filtering system may discard these reads before denoising even occurs. However, if those portions are removed, then those reads can be saved from the filtering step, albeit with slightly shorter lengths.

the_dummy · August 28, 2019, 10:41am

thank you for the explanation

Nicholas_Bokulich · September 12, 2019, 7:50pm

2 posts were split to a new topic: ITS analysis: does it make sense to use dada2 trunc-len parameters?

system · October 14, 2019, 2:04am

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