Good afternoon, everyone.
This is Ben Busby and I'm the genomics outreach coordinator and bioinformatics training lead
for NCBI.
I am joined by Peter Cooper who is the strategic communications coordinator for NCBI.
We will be talking about downloading human genome sequence, variants and annotation from
NCBI.
Today I will do most of this as a live demonstration but I prepared a set of slides covering most
of what I talk about as a backup.
The slides are available at this link, go.usa.gov/x58jN, as well as slideshare.net/benbusby.
On both of those resources there are other slides and presentations so feel free to check
them out or you can always Google for NCBI webinars.
If most of you are like me, you probably start your search with Google.
This is what we find most users do and one thing I might Google for is NCBI human genome
resources.
I can open up an Incognito tab just so I don't get autocomplete.
What I might Google for is NCBI human genome resources.
I don't know why my auto completes are still showing up, but that is not an issue for today.
The first link I see is human genome resources at NCBI.
We modified this page about one year ago.
We put a whole bunch of new bells and whistles in, and what we have done recently is moved
up the download section of the page and made it easier to use.
One thing you could do on this page is search for human genes and it will send you to the
NCBI Gene page and you can click on the ideogram to access the genome data viewer in that region.
What I want to talk about today is downloading various sequences as well as other NCBI resources
through this simple to use table.
If you want the latest reference genome sequence in either GRCh38, the new version of the human
genome, about 30% of you are using that at this point and 70% are still using the old
one, GRCh37.
If you are interested in the differences between GRCh38 and37, I would encourage you to check
out the genome reference consortium webpage.
You can do that by googling genome reference consortium and you can check that out and
it will tell you all kinds of things about GRCh37 and GRCh38.
Anyway, nn this page this gives you quick, direct links to download the reference genome
sequence, so this is going to be the FASTA file, gzipped, but that should be accessible
to most of you, as well as the gff3 file.
Here you can get all of the annotations that NCBI has for that file.
Some of you may just want RefSeq transcripts.
These are just the mRNA sequences that are transcribed from the GRC38 human genome, the
ones that we are fairly certain are transcribed.
You can get all protein sequences; this is a protein FASTA.
And you can also get a vcf for ClinVar.
This is a quick way to get it, as well as the vcf for dbSNP.
I'll make one word of caution, the dbSNP is rather large as you might expect, especially
since in dbSNP release 150 we doubled the number of RS numbers.
Finally, dbVar, which I think is really increasing in significance.
Those structural variants really have big consequences both in other technical work
with the human genome as well as well as clinical reporting consequences.
However, some of you may want API access to this kind of information for the human genome
or other genomes.
As many of you are probably aware, we have an API known to most people as E-Utils and
we've made a command line wrapper for that API called EDirect.
Still, it can sometimes be a little tricky to use, to make scripts for the commandline
wrapper so one thing we have done is we made a cookbook on github for scripts using that
command line interface.
The amazing thing to me is that we've made this interactive.
If you have a github account, you can put in issues for things that you might want to
do with our metadata API or you can just scroll down, copy some of these scripts and modify
them.
For example, if you want not just human but any taxonomic designation you can grab this
script and simply modify the query sequence and that would give you whatever taxonomic
designation you wanted.
It does say here for larger sets of data it may fail with a large number of arguments
and we find empirically that caps out at about 50,000 so searches for more than 50,000 items
probably won't work so well.
You can do a lot of similar things and if there is something you want to do with API
metadata crossing NCBI databases, try it and if you can't figure it out, once again put
in an issue in the cookbook.
The last thing I want to show you today is how to actually look at the human genome at
NCBI.
And for that what I would do is scroll down to the view portion of the page and I'm going
to load a resource we have called the genome data viewer.
And this really shows a lot of NCBI resources at the same time.
Here I can show a lot of RefSeq transcripts for particular gene loci.
I can show snps in ClinVar, dbSNP and I can also see RNA-seq coverage and that is pretty
neat.
If I want to I can use the tracks menu to split that out into various tracks.
One thing I really like about this browser is I can search for a disease or a gene name
and it will go ahead and load that.
I searched for ApoE and I can see the RefSeq isoforms for ApoE right here and I can see
related genes here.
You can also upload your own data or add tracks as you wish.
If you want to learn more, we have featured webinars and there are fact sheets.
Many people find these helpful and once again you can Google for NCBI webinars.
You can directly download the latest version of the human genome sequences Fasta as well
as annotation and associated files right here at the NCBI human genome resources page.
And with that I'm happy to stop and take any questions that you may have.
Somebody asked where you can find the common list of variants reported in all NCBI resources.
I would say if you are looking for short variants, under 50 nucleotides, you will want to look
in dbSNP.
And in fact for the dbSNP GRCh38 release, that's going to be a vcf of all of those variants.
Similarly if you are interested in structural variants, you will want the latest dbVar release.
Both of those resources are available right here on the human genome resources page.
There are some specific questions.
I will take a look at them and we may answer some of them off-line; yes, we will put them
in the documentation for the webinar.
All right.
We are going to go ahead and wrap this up.
Thank you very much for your time and I hope you have an excellent rest of the day.