Help for q2-cutadapt command

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1

Hello
I have used qiime2 2020.6 .I have de-multiplexed paired-end reads. Each fastq file included several primers with different lengths.
F1-TGGCGAACGGGTGAGTAA
F2-ACTCCTACGGGAGGCAGC
F3-GTGTAGCGGTGRAATGCG
F4-GGAGCATGTGGWTTAATTCGA
F5-GGAGGAAGGTGGGGATGAC
R1-CCGTGTCTCAGTCCCARTG
R2-GTATTACCGCGGCTGCTG
R3-CCCGTCAATTCMTTTGAGTT
R4-CGTTGCGGGACTTAACCC
R5-AAGGCCCGGGAACGTATT

I have read all topics and q2-cutadapt doc but I could not find how I can trim several primers by q2-cutadapt. should I use the q2-cutadapt command separately to remove each primer? or can I trim all primers with one q2-cutadapt command simultaneously?

2

Hi @Fatemeh_Abedini,

Welcome to the forum!

You are right, you can’t do this in one command using q2-cutadapt, so running it a bunch of times with a different primer each time is your easiest solution.

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