TypeLoader organizes its sequences in projects, which are a set of sequences with a common trait, e.g., a sample pool. This is neccessary, both to keep organized and also because ENA only accepts projects, not single sequences.
For the minimal sequence requirements, see => here.
To add a new target allele (a.k.a. sequence) to TypeLoader, choose the option "New Sequence" in the menu or task bar. This will open the New Allele dialog:
First, click "Choose XML or Fasta file" and choose the sequence file you wish to upload. This can either be a fasta file or an XML file like those generated by NGSEngine (see => Input Files).
Then, choose the project this sequence should belong to. If you have already selected a project prior to calling this dialog, this project is already pre-selected. If there is no project selected or you want a different project then the selected project, click "Choose a (different) existing project". If you have not started the project, yet, you can also click "Start a new project", which will open the => New Project Dialog.
Once you have entered a sequence file and a project, you can click the now green "Load" button. TypeLoader will then upload and read this file, which can take a bit.
Once the file has been uploaded, TypeLoader will take you to the next step.
If TypeLoader does not find the sample's ID in the raw file (it can be provided via a fasta sequence's header, see => Input Files), it will generate a popup dialog requesting you to enter the sample's ID:
Here, you enter the sample's internal ID (sample identifier within your lab - this is the main ID TypeLoader will use to identify the sample) and external ID (e.g., the sample identifier provided by the client) and click "Done" to proceed.
You can also enter the sample's provenance (use the => Settings dialog to specify preferred provenances, which will then be listed first in the dropdown menu) and date of collection here, or leave these empty to add them later. (You will have to enter them before ENA submission.)
If you get a popup dialog called "Manual choice of reference alleles necessary", please see => here for the next steps necessary before you can continue with uploading your allele.
If the uploaded file is a GenDX NGSEngine file, it contains multiple alleles of one locus. TypeLoader will ask you to specify which allele you want to upload:
Select one of the alleles by using the checkboxes.
Any allele marked by NSGEngine as "novel" is auto-selected.
Select exactly one allele. Now you can click "Proceed" and TypeLoader will take you to the next step.
Once TypeLoader knows which allele you want to upload, it will automatically annotate the sequence and generate the text file needed for ENA submission. This text is displayed for your information:
You can edit the text and use the "Discard changes!" / "Save changes!" buttons on the bottom to decide whether to discard or save your changes. (Usually, there should be no need to edit the ENA files.)
Do NOT change the identifier listed as cell line! This is the unique ID for your target allele and will be used to identify this allele in correspondence with ENA and IPD.
Once you're satisfied with the ENA text, click "Save new target allele".
TypeLoader will then save the ENA text as a file and all the details you have entered plus those inferred from the raw file to your user database.
By default, the following values are set:
- goal: novel
- allele status: ENA-ready
- lab status: completed
For NGSEngine XML files, the following values are set additionally:
- long read data: yes
For DR2S files which provide "software: DR2S" in their header, the following values are set additionally:
- long read data: yes
- long read phasing: yes
All of these can later be edited in the AlleleView.
Once TypeLoader finishes this step, the dialog is closed. Now you can find the allele in the => Navigation Area and view and edit its data in its => Sample View.
You can add multiple alleles of one sample one by one by specifying the same internal sample ID (the external sample ID of subsequent alleles of the same internal sample ID is ignored, to make sure to keep internal and external ID consistent with each other).
These alleles can be entered from the same raw XML file by uploading one allele, then uploading the same file again but choosing the other allele. Alternatively, a different raw file can also be used.
For more details see => Multiple alleles of one sample.
If you have several new fasta files you want to upload to one project, you can use the => Bulk Fasta Upload instead.
To avoid confusion and mistakes, TypeLoader does not enable this feature until you have gotten familiar with adding individual alleles.
If you ever realize you have made a mistake and need to change an allele's sequence after it has been uploaded to TypeLoader, see => Restarting an allele for how to proceed.