1.1. Is it possible to annotate samples in large batches starting from an existing text file or Excel spreadsheet with
sample names?
Yes, you can bring an Excel file into METAGENOTE by first selecting a package and once inside the sample group
table view, select Import from the main menu as shown here.
If you prefer to start from an empty template, we recommend you download the appropriate template from the MIxS
compliant templates used by NCBI.
1.2. How can I add ontology vocabulary to a field?
The ontologies available can be searched using the Right+Click option labelled Ontology search.
Once selected a box appears that allows users to enter keywords to find matches and import words to the table.
1.3. Can I add custom columns to my sample group table?
Yes, you can add custom columns in one of two ways: 1) Use Right+Click option Insert column right
or 2) Prepare a text file (or Excel spreadsheet) with the column headers you want, then proceed to import the table
into METAGENOTE (see FAQ 1.1). The custom column headers that don’t have a match in the selected
package will be appended to the sample group table.
1.4. Can I share a partially annotated sample group table with a collaborator?
Yes, simply press Export and METAGENOTE will download an Excel table that you can send. Once you have
completed the annotation, you can return to METAGENOTE and use the Import function to continue annotation or to start
the submission process.
1.5. What if I want to publish samples to an existing BioProject?
No problem, just add the BioProject ID to the column labeled as bioproject_accession. If you don’t already
find a column with such header, simply add a new column (Right+Click option) and label it as
bioproject_accession, then provide the BioProject ID to the samples you want to publish to that same
BioProject.
2. Submission
2.1. When I use METAGENOTE for publishing to SRA, will the BioProject submission show my name?
Yes, enter your full name and other contact details into the Description field. Enter either your name or the
group/lab name into the field labelled Project Contact Person or PI; this field will be displayed in the
BioProject and SRA records. Once your submission goes through, NCBI will send you an email to acknowledge your
submission.
2.2. Are the FASTQ files secure on your server and are they accessible to anyone?
When a user upload raw sequencing files, these go to a secure NIAID server from which they get transferred during
submission to the NCBI server using the Aspera client. The files are only retained in the NIAID servers for two
weeks to facilitate submission.
2.3. Is there a way to submit the metadata and files to NCBI but leave them on-hold (not public) until the time for
publication?
Yes, use the Hold Release Date field and put a future date. The sample metadata will not be visible to the public
until that date.
2.4. I have used Nephele for analysis. Is there an easy way to submit my Nephele files to SRA?
Yes! you can use the Nephele's metadata file to complete your annotation and submission directly from METAGENOTE.
Please watch this video on how to submit using your Nephele data to SRA.
3. Workspace
3.1. I see that people who are employees of NIH can register with METAGENOTE and get a Workspace to save draft sample
group tables. I am not an NIH employee but would also like to use this functionality, is it possible?
The METAGENOTE development team is considering opening up this functionality to all users in a future release but
as of now, please write to us and let us know if you are interested.
If you don’t have a workspace and you would like to store a table in draft format, we recommend that you use the
Export tool to download the partially annotated table. Later when you are ready to continue the annotation, use
the Import tool to upload the file with the partially annotated samples.