Dear Technical Support,
I try to create an annotated refseq which I'll be able to use for analyzing
my next gen seq data.
Because I'm interested in several hundreds genes I used the UCSC to create
chr coordinates for each exon of each gene which I'm interested in. The chr
coordinates had been used to design probes for capturing the genes.
To get the coordinates I uploaded a list of gene symbols and chose BED as
an output format. I had an option to choose number of bp to add at each
side of the exon and I typed 15-so I should get chr coordinates for all the
exons extended for the 15bp at each end (15bp exon 15bp).
I downloaded sequences and annotations for each of the human
chromosomes(hg19) from UCSC.
Then I created a gtf file with the coordinates and annotated them on the
refseq.
I got confused when I saw that the coordinates sometimes are created not
only for the exons.. - I attached few pictures so you can see what I mean.
The coordinates you can see as a pink bars.
Looks like the coordinates are sometimes for exons which doesn't exist...
Could you please explain me why did it happen and what that is?
Thank you
Best wishes,
Aga
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A Bierzynska
Academic Renal Unit
University of Bristol
[email protected]
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