trim.flows

Commands in mothur
1

Hi guys,

I am pretty new to mothur. I have some older 454 data sets that need denoising. I created my oligos file as described on the website, but the trim.flows creates an empty all.flow.files file? Has anyone else encountered a similar problem? the oligos file was in .txt format- I saw some tutorials online using it- could that be a problem? Otherwise how can I change this to an oligos format- if that is the problem?

my oligos file looks something like this:

forward AGAGTTTGATCMTGGCTCAG
reverse TTWGGTTTAATWGTACARCC
barcode ACTGCAGT P3.1.B
barcode ACTGCTCT P3.2.B
barcode ACTGCTGA P3.3.B
linker AGRGTTTGATCMTGGCTCAG


Thank you so much, Mel
2

Memory of trim.flows is a few years old. But are you sure you need the linker? look at a few seqs, where is your barcode in relation to the primer sequence?

3

Also, your linker sequence is the degenerate version of your forward primer. I suspect you want to ditch what you have as “forward” and replace it with what you have as your linker.

Pat