ITS fungal data processing

[Yogesh_Gupta (Yogesh)]

Hi,

I am trying to process the ITS data but with Itexpress tutorial I was getting some error at taxonomy assignment so I am trying to process it with without trimming by using this tutorial.

Fungal ITS analysis tutorial

Fungal ITS analysis, mock communities, and more fun NOTE: This tutorial was written in a QIIME 2 2018.11 environment. It is not guaranteed to work with earlier or later versions of QIIME 2. This tutorial was compiled as a working exercise for a QIIME 2 workshop in December 2018, and does not represent the only possible fungal ITS workflow with QIIME 2, or even a benchmarked protocol recommendation. See other tutorials, e.g., the q2-itsxpress tutorial for other fungal ITS analysis options in QII…

But the read quality look very poor, could you please advise how should I process this data.

read quality image is attached.

Thanks
Yogesh

[Nicholas_Bokulich]

Hi @Yogesh_Gupta,

@Yogesh_Gupta

I am trying to process the ITS data but with Itexpress tutorial I was getting some error at taxonomy assignment

The error you described in this topic has nothing to do with itsxpress, and everything to do with the taxonomy files that you are using. So you will run into that error even if you trim with cutadapt instead.

@Yogesh_Gupta

But the read quality look very poor, could you please advise how should I process this data.

Your read quality looks fine to me. Proceed as usual with selecting appropriate parameters.

Good luck!