Issue for generate shared file (for Subsampling)

Commands in mothur
1

Hello,
I am relatively new to Mothur. I am working with 454 reads (16S amplicons) and I want to normalize my data with subsampling and analyze it with Metastasts, for wich I am triying to generate a shared file.

I have already processed my data generating independent files for each sample after the splitting, so I have the following files for each sample:
454Reads.X.unique.nonchimeric.filter.phylip.dist
454Reads.X.unique.nonchimeric.filter.phylip.an.list
454Reads.X.unique.nonchimeric.filter.phylip.an.rarefaction
…

My problem is that I don´t know how to generate a shared file with this files. I also tried to start again for processing all samples together. But I have samples in two different libraries with repeated barcodes among the two libraries. So I can´t join the two fasta files and follow the 454 SOP protocol for trimming all samples at once.

Does anyone have any suggestions about how generate a shared file for subsampling this data?

Thanks you in advance,

Lucía

2

You essentially want to do everything we do in the 454 SOP. The one small difference is that you’ll either want to…

  1. run sffinfo, trim.flows, shhh.flows, and trim.seqs on your different runs and then pool the fasta, name, and group files
  2. run sff.multiple, which will do #1 for you.

Pat