Split fasta for use outside mothur

Integrating mothur with other programs
1

Hi, I need to generate a single fasta file for each of my samples for an analysis outside of mothur. Currently I have a fasta file with all my data, a name and a group file. Can I just use split.groups or does the name file have to be involved?
This is the output form shhh.flows if that helps

I am unsure of the way mothur stores the data and what role the name file is playing. Does the fasta file just have one example of each sequence, and then the name file denotes the how many copies of it there are. I need to capture this “abundance” information. E.g. so if this is the case I would need to reverse this. I need a fasta file with each of the seqs that came off the sequencer.

Does this make sense? I think sorting this is mainly a problem with my Google skills.

2

Hi RMW1,

The name & group or count file would tell you how many times each sequence was found. split.groups would work with a fasta and count file or fasta and names and group files.

You might also check out deunique.seqs. to go from a names and fasta file to a full fasta file.

Pat

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