How to clean Nextera paired-end libraries

–Hi,

my paired-end libraries were built using standard nextera transposase sequences as:

PrefixNX/1
AGATGTGTATAAGAGACAG
PrefixNX/2
AGATGTGTATAAGAGACAG
Trans1
TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG
Trans1_rc
CTGTCTCTTATACACATCTGACGCTGCCGACGA
Trans2
GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG
Trans2_rc
CTGTCTCTTATACACATCTCCGAGCCCACGAGAC

I’m not sure with the parameters i need to use in cutadapt step to clean my data, someone has already this command:

qiime cutadapt trim-paired --i-demultiplexed-sequences demux-paired-end.qza --o-trimmed-sequences trimmed-demux-paired-end.qza --p-cores 12 --p-anywhere-f CTGTCTCTTATACACATCTCCGAGCCCACGAGAC --p-anywhere-r CTGTCTCTTATACACATCTGACGCTGCCGACGA --p-front-f CAAGCAGAAGACGGCATACGAGAT --verbose

is it correct ?

thank you –

Hey there @lmanchon! I have no clue, I am not sure what I am looking at with the 6 sequences you provided above. Check out the cutadapt docs for more info on how cutadapt works, this will be the clearest path for you to move forward. Please report back on what you find! :qiime2: :t_rex:

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