Processing uBiome RAW files

Today the option to download as JSON or CSV disappeared from the uBiome site. The ability to download the raw sequence data was there.

Over the last 30 minutes, I processed one of my samples via https://metagenomics.sequentiabiotech.com/ . (Which offers free accounts – up to 2 GB of data, the download files from uBiome uploaded is just 12 Megs, so the free account will work for most people.)

The main thing is for people not to go into a panic. It appears that uBiome is planning to add back the download options. If they do not, there are possible alternative solutions.

My Samples Listing for ONE ubiome sample

It generates many files, for example below are some of the files sample. uBiome does 4 passes, and the numbers from each pass is shown below. How you boil the four numbers into one is an art – arithmetic mean, median, geometric mean, etc are possible choices.

species.count
strains.count

I look at my ubiome JSON file for the same data and I get:

  • Bacteroides acidifaciens 30655
  • Bacteroides faecis 38174
  • Bacteroides finegoldii 21914
  • Bacteroides ovatus 192887
  • Bacteroides sp. J1511 91
  • Bacteroides sp. ‘Smarlab BioMol-2301151’ 30
  • Bacteroides thetaiotaomicron 153659
  • Bacteroides vulgatus 30

This is not surprising, because the raw data fragments are looked up in different reference databases. By the way, there was no E.Coli listed here either!

Bottom Line

I will do a walk thru video this coming weekend for people interested in exploring a different analysis of the raw data. It is a multiple step process that takes about 30 minutes per sample.