How to remove primer with different length

[Nicholas_Bokulich]

@Lei

The sequencing center told me that they have already remove barcode. So what I need to remove is the primer (showing the letter after dash in the image).

Since the barcodes are removed, the concerns about demultiplexing that @Mehrbod_Estaki raised are no longer a concern.

You can absolutely use QIIME 2 to accomplish your goal of removing the primers and variable spacers. Just use cutadapt once; since the variable spacer is at the 5' end of the primer, just use the primer as the "front" adapter with cutadapt trim-single and the primers (and all preceding bases, including the variable spacer) will be removed. See the tutorial here and use the --help flag to see the full usage details for cutadapt:

Demultiplexing and Trimming Adapters from Reads with q2-cutadapt

NOTE This tutorial is a work in progress, and is incomplete at the moment. It demonstrates at a high level some of the methods available in the q2-cutadapt plugin available in QIIME 2 2018.2. Please stay tuned here for additional updates as this tutorial is expanded upon in the coming weeks. Multiplexed reads with the barcodes in the sequence reads can be demultiplexed in QIIME 2 using the q2-cutadapt plugin, w…