Removing Chimeras problem.

Commands in mothur
1

I am using 16S data that give me an initial .sff file. I have two points where I am getting stuck.

1: If I am using my own data, where does the .oligos file come from? I just left it out and continued (hopefully) without error. Is this valid?

2: On the “Removing chimeras” step, I am getting en error message from a blank .accnos file.

It says 0/6 chimeras found.

it says “F10test.shhh.trim.unique.good.filter.unique.precluster.uchime.accnos is blank. Please correct.”

My thoughts are to just go past without removing chimeras because I am trying to learn the program. Or, to use a .accnos file from the tutorial to see if there is another error other than the .accnos file, then try to track it down. I have screen shots and the code I have entered if that would be more helpful.

Thank you for any help/advice you can provide. Have a great day.

2

1: If I am using my own data, where does the .oligos file come from? I just left it out and continued (hopefully) without error. Is this valid?

You need to create this yourself based on the primers and oligos that were used by your sequence provider.

2: On the “Removing chimeras” step, I am getting en error message from a blank .accnos file.

It says 0/6 chimeras found.

I suspect something weird is going on. I think you only have 6 sequences at this point. This probably means that something happened along the way that shouldn’t have happened.

Once you get the oligos file figured out, run back through everything and see where you get. If you can post specific command syntax we can help further.

Pat