Oligotyping and MED

Thank you, Kristen! These changes look appropriate to me and we will see if things break for others :

Also had this problem! Would be keen to hear if you managed to get further with it? On Monday, 30

Hi all, I was testing MED pipeline with my data and wondered whether I should change -n (default is 4

Your description of the difference is correct :) On Thu, Aug 29, 2019, 3:58 PM Courtney Swink <

Thanks so much, that fixed my problem! On Wednesday, July 31, 2019 at 10:28:35 PM UTC-4, A. Murat

Meren, Thanks for getting back to me so quickly. I really appreciate you passing on this info to me.

Hi Meren, I've been having trouble with MED removing many reads during decomposition. In a

Hi Hilary, I don't know why heatmap.R is not in the path. It should be in a proper installation.

Hello everyone, Can anyone tell me what exactly this error means (qiime1) [qiime1@localhost

https://www.google.com/search?q=how+to+use+dada2 -- A. Murat Eren (meren) http://merenlab.org ::

Hi Hilary, You're right. The checks should be done before the analysis starts. I will do

Hi Rodrigo, I haven't tried any further, but still waiting for a hint or response by Eren. Either

Hi Meren, First of all, thank you very much for your work on oligotyping . I really enjoyed reading

Hi there, i'm doing oligotyping on Fungal ITs datasets. I would like to know how the different

Dear Meren I am sorry for my deed and thank you for your advise. We could able to fix the problem.

The oligotyping pipeline does not have a specific tool to re-format a given FASTA file (it has a

Hi Rachel, Were you able to perform oligotyping with fungal sequences? If so, have you been able to

Hello all, On the MED index.html result sheet the field "Nodes agglomerated based on co-

Thanks, but because the MED page mainly refers back to the oligotyping tutorial I figured somehow

Hello, You could try editing the taxonomy file (_tax_assignments.txt), where the word Synechococcus

Bit late to the party, but thought I'd add my experience with the MED pipeline to hopefully help

I thinks it does not working because NCBI switch the IP address (from http to https) If you will fix

Hi Ed, Do you mean the -c parameter in the oligotyping pipeline? If yes, the answer is no :) -d, the

Hi Meren, I also experience this problem when multi-threading the oligotype command on Biolinux with

Sorry! I clearly misread your question. Yesterday was a very busy day :/ OK. I'm not sure why it

Hi, Please make sure you are using v2.2 (decompose -v). That search is done to find outliers in final

What does the RUNINFO.log file says? Are there any errors in it during the creation of some of these

Dear Murat (Meren?), I've been discussing it with a previous colleague of mine (developer of

SO I used that script : o-pad-with-gaps and perform the alignment but I got a weird error: align_seqs

But that page is my opinion :) It explains exactly how I would have done it. I'd start one or two