Tip:
Highlight text to annotate it
X
Let's do that.
I will go to the Genome menu and select
Create .genome File.
I will call this genome HCV.
I am going to find a FASTA file by browsing.
And then we'll click OK.
It says that it will create the
genome file in the desktop.
I'm going to select my folder within the desktop where I
want the genome file to be.
Save.
Now I have my HCV from NCBI.
The chromosome name is H77.
That's the annotation that I had in the FASTA file.
And the entire sequence is over nine kb.
Now I want the annotations.
I will do File, Load Profile.
I will pick the BED file.
OK, here's my BED file.
Now I have my genome's annotations.
Because in the zoomed out view everything is so clustered
together, I can do a right-click
here and pick Expanded.
That will give me a different view where I can see each of
the protein products.
Now that we have the genomic sequence as well as each of
the annotations, I can proceed to import my data of interest.
If you actually zoom in before we do that, we
can zoom into a gene.
You can see that it has the actual sequence as well as the
annotations.
So let me zoom out so you can appreciate
when we load the data.
And we're going to bring in a BAM file with sequence data,
which is right here.
Notice that it has the BAM.bai file, which is the index file
for the BAM, in the same folder.
That is important.
Click Open.
Now this is my sequence data.
I can zoom in, and you will be able to see the reads-- each
of the gray bars is a read--
with the base pairs that are in contrast to the annotated
genome, meaning a SNP in this case.
I can also bring other file types, for example a VCF file
with variants.
I have one right here that was a
combination of various files.
So now I have variant calls annotated for different
samples in my VCF file.
And I can see how many of the samples contain this
particular variant.
And that is in my NS5B RNA-dependent RNA polymerase
gene that was provided within the annotations BED file.
And this is all I wanted to show you for now.
Thank you.