To visualize your own data, there are two options to do this. If you have a BAM
file but have not yet generated a readable XML file, select the "Generate Data"
option. If you have already generated a readable XML file, you can directly
upload these XML files by selecting the "Upload Data" option. You can enhance
these options by storing your visualized data onto your private account (see
more in the
"Manage Person Account"
help card)
Generate Data
This opens a form to fill which generates an XML which is readable by the
eFP-Seq Browser to visualize your data. Any field with an asterisk at the end of
it are mandatory fields to be filled for your data to be visualized properly
(without it, the eFP-Seq Browser cannot visualize your data).
The following table describes what each field requires:
| Form Label |
Form Input Description |
| Dataset Title |
REQUIRED* The title of your entire dataset. This will be displayed
on the navigation bar in the dataset dropdown option if you chose to
store this dataset to your private account
|
| Author(s) |
REQUIRED* You and/or any other authors that contributed to the
dataset
|
| Contact info |
The contact information of the authors |
| Title |
REQUIRED* The given title for each individual BAM entry/file. It is
recommended that this entry is kept short
|
| Description |
REQUIRED* A written description of each individual BAM entry/file
|
| Record Number |
The SRA/SRR record number/identifier for the individual BAM
entry/file
|
| RNA-Seq Data/BAM file Repository Link |
REQUIRED* A link to your individual RNA-Seq Data/BAM entry/file
repository. The eFP-Seq Browser can read BAM files stored on either
Google Drive
or
Amazon AWS. Each BAM file must be in its own folder with its BAM index file
|
| BAM Filename |
The filename of the BAM file in the repository location (with the
.bam file extension)
|
| Publication Link |
A link to the published research |
| Sequence Reach Archive/NCBI Link |
If the record number has a website describing it in more detail,
that link can be posted here
|
| Total Reads Mapped |
REQUIRED* The total number of reads in the BAM entry/file. A read
refers to a sequence of base pair(s) corresponding to all or part of
a nucleotide fragment. If you do not know how many total reads
mapped there are in your BAM file/entry, just insert 0 or leave it
blank and the eFP-Seq Browser will find this value for you (NOTE: If
you do input 0/blank, this will significantly increase load time).
|
| Read map method |
A description of the method that was used to map the read alignments
|
| Species |
REQUIRED* The organism that your RNA-Seq data is mapped for.
Currently, the eFP-Seq Browser only supports
Arabidopsis thaliana
|
| Tissue |
REQUIRED* The tissue part that your individual BAM entry/file
RNA-Seq data is mapped to. If you do not know what tissue it is
mapped to or your species is not Arabidopsis thaliana, it
is recommended you select the "Other" option
|
| Controls |
The BAM record/experiment number of the controls in your RNA-Seq
data. Separate controls by commas
|
| Replicate Controls |
The BAM record/experiment number of the replicate controls in your
RNA-Seq data. Separate controls by commas
|
If you wish to reset the form and return it the default empty form with one
entry, you can click on the "Reset Form" button to do that.
If it is easier for you to fill an Excel (XLSX) template (which you can save and
continue at any time), you can
download our Excel template
to generate the readable XML and then click the "Upload Excel" button to fill
the form out.
For the most part, the Excel template follows the same format as the form with
the exception of the hidden field "Tissue subunit*" which in the Excel template,
you are going to have to fill manually.
For the column "Tissue subunit*", there is a dropdown of options that correspond
with the tissue that you select. Please fill it appropriately with the correct
option name from the dropdown. If you do not fill this correctly, this will
default to either "all" or a respective correct tissue subunit.
NOTE:
For the Excel template, it is recommended for the following columns
you do not manually type in your options but rather use the Dropdown
option as it will prevent any errors from arising:
- Repository type*
- Species*
- Tissue*
- Tissue subunit*
To convert the Excel data, copy and paste your fill Excel template into the
"Upload Excel" form (in Excel, Select all and then in the eFP-Seq Browser's
Upload Excel, Paste), click the "Convert Data" button and let it load. If your
Excel data has more than 50 datasets, it may take >5 to convert the data and the
eFP-Seq Browser will be unresponsive during this time.
NOTE:
For the Excel converter to work correctly ("Upload Excel"), you need
to also insert row 1 of the of the Excel template:
"Title* Description* Record Number * RNA-Seq Data/BAM file
repository link* BAM Filename* Repository type* Publication Link
SRA/NCBI Link Total Reads Mapped* Read Map Method Species* Tissue*
Tissue subunit* Controls Replicate Controls"
Upload Data
Once you have an XML generated for your data, you can directly upload it to the
eFP-Seq Browser at any time. To do so, click on the "Upload Data" button in the
navigation menu on the left side of the eFP-Seq Browser.
If you are logged into your private account, you will be prompted with the
option if you want to upload the XML to your private account. If selected "YES",
then this XML will be accessible at any time you are logged in without the need
to upload again.
If you wish to learn more about the XML file and its attributes, you can check
out the
"XML Parameters"
help card or if you wish to learn more about your private account and how to
manage it, you can check the
"Manage Personal Account"
help card.
Submit data for community use
If you would like to have your dataset publicly available to all users, you can
send your generated XML to nicholas.provart@utoronto.ca for us to review and
possibly add for all users to access.
