merge sff from different runs

Commands in mothur
1

Hi all

I had the same sample sequenced with same barcode in two runs. So I got two sff file for the same sample. when I want to denoise the sequences, Should I firstly merge the sff files together and then denoise once, or denoise them separately and merge them later?

Appreciate for any suggestion!

Thanks

2

I would run the SOP on each run separately through chimera checking, then merge

3

Actually… you would want to pool them after trim.seqs to make sure they are aligned the same way. We actually have a command that does this for you: sff.multiple (http://mothur.org/wiki/Sff.multiple).

Pat

4

Hi Pat

Thanks！ That helps a lot

The problem is that some sff file contain few sequences (~5000 sequences). For example, Sample 1 has two sff files. One contains 35000 sequences, the other contains 5000 sequences. As I know shhh.flows will denoise each flow file separately. Will denoising with shhh.flows command be effective with such small data sets?

5

Thank you

6

ah right forgot to say that I realigned them after merging. Chimera checking can be computationally expensive, I didn’t want to repeat that step for all samples each time I got a new batch of sequences