Data import

Commands in mothur
1

Hello,

I am actually a newcomer to Mothur but have so far at least gone through all steps in MOTHUR using one of our data files. Now, here are my two main questions:

  1. We are doing tag-encoded 454 pyrosequencing for analysis of microbial communities on plants. Now, from our sequencing service we receive .sff files separately for each tag (=sample, referred to as MID). So, for a given project, we have eg 44 single .sff files each containing eg 1100 sequences from the different organisms discovered in each sample. These samples should be now compared in MOTHUR. If I understand it correctly, for Mothur analysis I need one file containing all lets say 40.000 sequences from the different samples. Is there a feature to combine the sequences in one data file later during the analysis or even before the actual analysis?

  2. So far, we are using the program MEGAN for analysis of our data. MEGAN imports BLAST files in the .rma file format. Is there any way to directly import these .rma files into MOTHUR as this would save some time during the pre-analysis steps?

Any help is greatly appreciated!
Best regards from Germany
Annette

2
  1. We are doing tag-encoded 454 pyrosequencing for analysis of microbial communities on plants. Now, from our sequencing service we receive .sff files separately for each tag (=sample, referred to as MID). So, for a given project, we have eg 44 single .sff files each containing eg 1100 sequences from the different organisms discovered in each sample. These samples should be now compared in MOTHUR. If I understand it correctly, for Mothur analysis I need one file containing all lets say 40.000 sequences from the different samples. Is there a feature to combine the sequences in one data file later during the analysis or even before the actual analysis?

You would run each sff file / oligos file combination through trim.flows, shhh.flows, and trim.seqs and then merge the outputted fasta, names, and groups files. I know this is cumbersome, we are working on a single command to do all of this for you, but it won’t be until the next release.

  1. So far, we are using the program MEGAN for analysis of our data. MEGAN imports BLAST files in the .rma file format. Is there any way to directly import these .rma files into MOTHUR as this would save some time during the pre-analysis steps?

No - in general, we’re not big fans of BLAST as it does a pretty lousy job on 16S sequences.

HTH,
Pat

3

Hi,

I was wondering whether you had considered adding an option in mothur to export files in BIOME format such as that can be exchanged between MG-RAST, QIIME and MEGAN?

It might be a very handy feature, especially for loading mothur files into MEGAN.

Thank you,

Chris

4

http://www.mothur.org/wiki/Make.biom

5

Thank you!