One vs two adaptor sequences using cutadapt

General Discussion
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1

For a paired end data, i have one adaptor sequence in the sample sheet as per the kit. However, cutadapt trimming step requires me to provide 2 adaptor sequences (--p-adaptor-f and --p-adaptor-r). How to provide 2 adaptor sequences if there's only one provided

2

Hi @Pratyusha_Patidar, Those two parameters are optional, so you can provide only one.

3

Thank you @gregcaporaso. In that case what will be the command for adpator sequence, --p-adaptor or --p-adaptor-f or--p-adaptor-r ?

4

Hi @Pratyusha_Patidar, if your goal is to simply remove primers from your sequence then all you need to provide is the --p-front-f and --p-front-r, as these are for removing sequence from the 5' end of the reads and any sequence before it. The --p-adapter-f and --p-adapter-r, are for finding and removing sequence at the 3' end of the reads and any sequence after it.

You can type qiime cutadapt trim-paired --help for more details on the commands.

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5

Thanks @SoilRotifer for clarifying :slight_smile: Same noted.

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