FASTQ uploads from other labs

  • How do I upload my FASTQ data from another lab?

    Youtube Video walkthrough of the process Register an account with us at Biomesight. Once registered, validate your email address and go to: My Samples - Upload Files. Complete the sample upload form, including selecting the files from your sample. Do not rename the original file names as obtain...

  • Which labs are currently supported?

    We currently support FASTQ uploads from uBiome ThryveInside Psomagen (16s) - Note we do not support their shotgun sequence data. Olawell Some of our users have also successfully uploaded samples from RedLabs in Belgium and others. The main requirement is that the reads must be split between forw...

  • Which sample types are accepted?

    We allow for the upload of gut, vaginal, oral and skin sequence files, but note that our website interpretation apply only to the gut microbiome. You can still benefit from obtaining an alternative analysis (e.g. CSV download and advanced sections for samples from other areas).

  • When will support be added for CSV uploads?

    We've had requests from our users to support the upload of CSV uploads and this feature is currently under consideration. Re-analysing FASTQ data allows for a better foundation to compare data between labs (although still many differences possible) so we prefer this method. If enough of our custo...

  • Can GI Map or GI Effects data be uploaded?

    No, this is not possible as we would not be comparing similar technologies.

  • Are there any specific browser or operating system requirements?

    As we're a small development team, we develop and test only on Google Chrome so you will have the best experience using  Chrome. You can try using other browsers like Edge, Firefox and Safari but if you are having any UI issues, it would be best to use Chrome. Note that Internet Explorer is NOT s...

  • Common Analysis Differences compared to Ombrelab

    At the time of writing this article, we're commonly seeing the following 2 species in uploads from Ombrelab that are not included in the Ombrelab results or csv. Bilophila wadsworthia Bifidobacterium longum Users are also seeing lower relative abundances of these after uploading from Ombrelab: A...

  • FASTQ file size checks

    Many users, especially those using Safari, download incomplete FASTQ files from Ombrelab. As this is not on the Biomesight platform, it's not something we can comment on any further. We check for a minimum file size of 2.5MB, which is a conservative file size as most filesets are larger than this...

  • How to download FASTQ files from Ombrelab

    Log into your account at Ombrelab. Go to "My kits" Look for a button called "Download FASTQ". This is available under each sample. When you click on "Download FASTQ" you will get a pop-up form from where you need to download both fastq1 and fastq2. Do not rename any of the files. The original fil...