How to get start to analyse 18S

1

Hello, I`m TAKA.
I am Japanese, so please forgive my poor English.

Ill analyse 18S metabarcode data of eukaryota by illumina. I read examipation of Miseq SOP and run test data by mothur, I can run enough. But when I run for my original data of 18S, I cant prepare reference date set.

On Mothur Miseq SOP, it needs following 4 files.
①Latest version of mothur. You will most likely not need the version with “tools” in the name.
②Example data from schloss lab that will be used with this tutorial. It was extracted from the full dataset
③SILVA-based bacterial reference alignment
④mothur-formatted version of the RDP training set (v.9)

I think ① and ② are OK, and ③ is replaced by “silva.bacteria”.
But I cannnot understand how to change ④.

Please help me …

TAKA

2

Hello,

Though I am not an expert, I think the RDP training set mentionned in the SOP (your point 4) is not suited for analysis of 18S eukaryote sequences. I hope I am not mistaken but I did the classify.seqs with SILVA alignment and taxonomy.

Yours,
Maxime

1 Like