[Genome] Downloading annotations for parts of genome

[Goel, Manisha]

Hello,
I have a large number of D.melanogaster genome co-ordinates for which I
want to download the annotations.
Or more specifically I just need to know if the region denoted by these
coordinates is annotated as "repeats".
I have tried looking through the table browser, but am unable to figure
out if I can do this using table browser.
Could you pelase suggest the most straighforward way of getting this
information from ucscs genome browser.

Thanks a lot for your help.
-Manisha

[Kayla Smith]

Manisha,

If you are looking to download sequence, here is a link to our FAQ on
how to download sequence in batch from an assembly:
http://genome.ucsc.edu/FAQ/FAQdownloads#download32

When using the table browser to output sequence, there is an option
under "Sequence Formatting Options" to mask repeats to either lower case
(or to N). If you select this option before clicking on the "get
sequence" button, then the repeat masked sequence will show up in your
results as lower case, and everything else will be upper case.

Additionally, you could intersect your genomic co-ordinates with repeat
masked data to see if there is any overlap between your coordinates and
repeats. To do this in the table browser, you could:

1. Save your genomic co-ordinates as a custom track

2. In the Table Browser, set:
clade: insect
genome: D. melanogaster
assembly: Apr. 2004
group: Custom Tracks
track: User Track
table: (what ever you had named your custom track)
click on create intersection
group: Variation and Repeats
track: RepeatMasker
table: RepeatMaster (rmsk)
Select the radio button that says "All User Track records that have
any overlap with RepeatMaster"
Click "submit"
output format: BED
click "get output"

3. Your results will be those of your items which had any overlap with
RepeatMasker.

I hope this is helpful to you. Please don't hesitate to contact us
again if you require further assistance.

Kayla Smith
UCSC Genome Bioinformatics Group

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