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In this video, I'm going to show you how to upload custom data tracks for viewing in
the NCBI Epigenomics database. First, from the Epigenomics home page, select Upload
Tracks from the Epigenomics Tools section.
You must have, and be signed in to, a My NCBI account to upload your tracks. This maintains
data privacy and supports long-term data storage. Accounts are free and may be established in
the My NCBI part of the site, or by clicking on this Sign in/ Sign up button. I'll
use the button and sign in directly to NCBI.
You now have a page with both required, see the asterisks, and optional fields to complete
prior to beginning the upload. You may want to specify a track name so that it will display
later on in the genome viewer, and one of these file types, or let the program auto
detect the file type. In my example, I'm going to upload a data track for histone H3
lysine 4 trimethylation that has been assayed in human fetal lung tissue. So, I'll add
the track name, leave File Type on auto detect, and use the Choose File button to specify
my local wiggle file, but I could select URL to input an online file location. Notice that
you can upload compressed files generated by gzip (.gz extension), by bzip2, and by
lso.
I'll leave Species set to *** sapiens, and since my data were aligned to the most
recent genome assembly, I'll select GRCh37.
This Feature type field has an autocomplete function, for example, I'll type in h3...k4
and select the trimethylation. You can also use more general terms, like histone modifications,
DNA methylation, chromatin accessibility, or other free text.
These optional metadata fields are also available.
I'll enter lung in the tissue type field, then click More to expose additional
fields, and enter fetus for Developmental Stage.
Okay, I've completed all the fields, so I'll click the Start Upload button.
This opens a new page with a status bar. It may take several minutes to upload larger
files. When complete, you will see a few options, including uploading another track. I want
to view my track in the genome viewer so I'll click View on genome. I'm interested in
the gene SFTPB, which encodes the lung specific surfactant protein B, so I'll enter
this in the gene or location box and click Go. Now I can view my uploaded data at this
locus.
I can add additional data tracks into this display, either by repeating the upload process
here, or by browsing for files in the Epigenomics database. Let's say that I want to see how
my data compares to other data tracks from lung tissue. I'll click the browse button,
which takes me to the Experiment Browser interface.
As you can see, my uploaded track appears in the first row of the table, and all uploaded
tracks are stored in the My Uploads collection on the left side of the page. Please
note, that since I am signed into My NCBI, this track is only visible to me and is maintained
completely private. When I sign out of My NCBI, the track will no longer be visible.
I'll select my uploaded track, then to identify other lung tissues I'll use the Biological
source filter and select lung, fetus. Since I am interested in H3 lysine 4 trimethylation,
I will select these two tracks that examine the same feature.
After selecting the desired tracks, I'll click View on Genome, then, if necessary, enter
my gene of interest, SFTPB. It may take a minute for the tracks to display. But, now
I can visually compare my data with the other tracks.
That's it for uploading your own data tracks. We have other videos on the Epigenomics database
at the URL shown, http://www.youtube.com/playlist?list=PL5325E662E57F9E7F.
Click on the note to go to that video playlist.