search

mothur / mothur.github.io

wiki for the mothur software package
https://mothur.github.io
Creative Commons Attribution 4.0 International
19 stars 20 forks source link

Customized 5.8S-ITS2 sequence for trimming silva seed reference. #106

Closed zhinew15 closed 1 year ago

zhinew15 commented 1 year ago

Hi all,

I am having trouble finding the sequence of 5.8S-ITS2 to trim the silva.seed_v132.align database. I found the primers my project used from Taylor et al., 2016 (doi:10.1128/AEM.02576-16), blasted the primer, but it didn't work. What else should I do?

pschloss commented 1 year ago

The silva database only has 16S and 18S rRNA gene sequences. There are no ITS sequences in there.

Pat

On Fri, Jun 2, 2023 at 3:26 PM zhinew15 @.***> wrote:

Hi all,

I am having trouble finding the sequence of 5.8S-ITS2 to trim the silva.seed_v132.align database. I found the primers my project used from Taylor et al., 2016 (doi:10.1128/AEM.02576-16), blasted the primer, but it didn't work. What else should I do?

— Reply to this email directly, view it on GitHub https://github.com/mothur/mothur.github.io/issues/106, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJUUBFTNSZJM6VSQ7X45MTXJI45NANCNFSM6AAAAAAYYWR3UY . You are receiving this because you are subscribed to this thread.Message ID: @.***>

zhinew15 commented 1 year ago

Oh, thanks Pat!