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cozygene / FEAST

Fast expectation maximization for microbial source tracking
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How to use existing data as source? #56

Closed AkilaMuthalagu closed 1 year ago

AkilaMuthalagu commented 1 year ago

I have indoor samples where humans are the only source. I want to use already available data sets, such as skin microbiome data, gut microbiome data, etc., with mine to understand how much fractions come from humans. However, only fastq files are available, not the OTU count files for those existing data. Would anyone happen to have an idea about how to move forward? I have done a lot of reading and not moving further. Any suggestions would be highly helpful.

Thanks Akila

abossers-uu commented 1 year ago

If you only have fastq files from different studies. Try to obtain the OTU tables from those studies. If you cannot get them, you'll have to run for instance dada2 yourself to obtain such an otu table.

Subsequently you'll need to merge the otu tables from the different studies. Be sure this this is done in a way compatible with different ASVs and do not get blinded by shortened ASVxxxx or OTUxxxx or Taxxxxx numbered indices. It will result in rubbish. See dada2 documentation for more details.

AkilaMuthalagu commented 1 year ago

I will do. Thank you