Hi UCSC Team,
I work with genomic array data and try to find out the best way to get
sequences from my array annotations.
For example I have got the information that in a DNA sample the region
Chr1:112,687,850-112,693,696 is deleted.
In my last Data set the annotation data was given with the hg18 assembly and I
found the "Extended DNA Case/Color Option" page the best way to deal with my
data. I just copied the coordinates of the region of interest in the
"position"-field and the result was the sequence of interest. That was nice!!!
However, in our new array data set the data is given with the hg19 assembly and
here are the problems:
In the "Extended DNA Case/Color Option" I can not change between the different
assemblies so now I have to translate the sequence annotation data but this
feature does not work with every sequence and often results in error messages.
Then I tried to go via the genome browser. The genome browser gives me a nice
overview either with the hg18 or hg19 assembly. But it does not show me the
sequence underlying the search and I can not find a button or link or track
leading to my sequence of the given coordinates (because here the track "your
sequence" like in the Blat-search when you use sequence-data as input, is
missing).
Is there a user friendly tool that makes a simple sequence output, when using
coordinates like Chr1:112,687,850-112,693,696 as input and let you change
between different assembly versions?
Thank you for your answer in advance,
Regards,
Axel Weber
_______________________________________________
Genome maillist - [email protected]
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