Issues with group/oligos files

mothur bugs
1

Hello all,

First I should say that I am entirely new to this whole program and wading through uncharted waters for our lab. I am following 454 analysis example from the main website to test our data. I am running into a problem when it requires a group file. I am sorry if this is a fairly easy fix, but again, I am entirely new to all of this.

When I started the analysis, mothur would crash when trying to run the shhh.flows command. So I opted to take the trim.seqs approach as it says to. I do not have an oligos file (at least that I am aware of) from the lab that did our sequencing. It seems that because I neglected to enter an oligos file, I did not get a group file from the output? I tried to get this file in an output several times, but never was able to. It didn’t seem to make a difference until I got to the OTU analysis part of the tutorial, making the cluster and shared file.

Is there any suggestions on how to get around this in order to continue the investigation? Is there another name or form for the oligos file that I am just not aware of? I am very appreciative of any advice.

Thanks!

2

You have to have an oligos file. This is essential to remove the barcodes and primers from your sequences. You make the oligos file with the information that the sequence provider gives you. Badger them until they tell you your barcodes and primers. If you’re not sure how to format those into an oligos file post them here and we can help. This is also probably why your shhh.flows failed.

Pat

3

Thanks for your quick response!

I did nose through our info last night and did manage to find the primers and barcodes. We have two of those files though; one has columns for our ID, a description, barcode sequence, linker/primer sequence, barcode name, and project name, while the other has all of those plus an empty column, titled repeats.

Thanks

4

http://www.mothur.org/wiki/Oligos_File

5

Thank you very much! I copied the barcode and primers into a text file and it appears to be working. I just tried to match the format of the oligos in the SOP file.

Thanks again!