MED output into QIIME

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sfeds

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Jun 7, 2016, 6:09:23 AM6/7/16
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Hi,
I'm working with a sequencing facility that provides as sequencing output a MED file (based on minimum entropy decomposition).
Would it be possible to transform this data into a BIOM file so I can go into QIIME for further visualization/analyses?
Thanks!

abir...@gmail.com

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Jun 7, 2016, 8:01:59 PM6/7/16
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Hi, 
Assuming you have the MED counts file (analogous to matrix_counts.txt from the sample MED results at http://oligotyping.org/MED/files/sponge-html-output/ ), you should be able to convert this to a biom-formatted file with a command like this:

biom convert -i matrix_counts.txt -o matrix_counts.biom --table-type="OTU table" --to-hdf5


where matrix_counts.txt is the name of your counts file from MED and matrix_counts.biom is the name you want to give the biom-formatted version of this info.  


Note, however, that you won't have taxonomic info in this biom table, which will cause problems if you try to perform downstream analyses based on taxonomy such as summarizing taxa in core_diversity_analyses.py .

Best,

Amanda

sfeds

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Jun 9, 2016, 4:21:45 AM6/9/16
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Hi Amanda,
many thanks for your answer, very helpful.
Indeed I thought converting wouldn't be too problematic, thanks for the line of script.
However I do need to make downstream analyses. In my MED output I have 7 taxonomy levels (plus species), is there any way to transform this into "QIIME friendly" data?
Otherwise there's not much I can do with the data.
Thanks

abir...@gmail.com

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Jun 10, 2016, 1:43:20 AM6/10/16
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Hi, 
Yes, if you have the taxonomy information, you can add it to the biom table created earlier; once this is done, you should be able to analyze it in the standard ways.  You will need to use a command of the format 

biom add-metadata -i matrix_counts.biom  -o matrix_counts_with_taxonomy.biom  --observation-metadata-fp my_taxonomy_info.txt

where matrix_counts.biom is the output of the previous command I sent and my_taxonomy_info.txt is a file of observation metadata containing at least a column containing OTU ids and a column containing their taxonomies; see http://biom-format.org/documentation/adding_metadata.html for more details, including on the format of the taxonomies.
Best,
Amanda

sfeds

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Jun 10, 2016, 2:20:24 AM6/10/16
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Many thanks Amanda, wonderful!
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