Reg: Query regarding CPG island file

[Ajay Katoch]

Dear UCSC Team,

Good afternoon!

I am hereby trying to get the cpg-Island sequences for methylation microarray data and stuck at a point, if you can help me out to resolve the issue.

I am using Agilent Genomics Workbench software for Methylation Microarray experiment, while getting the output files the software asks for CPG-Island file with respect to the chromosome coordinates to generate outputs.

I am trying to download CPG-island sequences for the coordinates from UCSC browser, please correct me if I am wrong

I have attached two files with the mail, please have alook on them and help me out.

Thanks and Regards,
Ajay Katoch

 -- 
Warm Regards
Ajay Katoch
Junior Scientific Analyst
Microarray Analysis
Genotypic Technology Pvt Ltd
#2/13, Balaji Complex, Poojari layout
80 feet road, R.M.V. 2nd stage
Bangalore 560094, India.

[Christopher Lee]

Hi Ajay,

Thank you for your question about obtaining CpG Island data from UCSC.

I am a little unsure as to what you are asking. Are you trying to get the hg19 genomic
sequence corresponding to the locations listed in your "Sample file.txt"? If so then
then steps listed in your PowerPoint file are indeed correct: Load the custom track in
the Table Browser, select "sequence" as your output format, and click get output.

If you are worried about your ~200,000 line BED file timing out while grabbing the sequence
from the Table Browser, I was able to upload a 200,000 line BED file custom track to the
Table Browser and download the corresponding sequence, although your results may vary
depending on how far away from our servers you are.

Please let me know if this is not what you are asking and I will help you further.

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any
further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address
are archived on a publicly-accessible forum. If your question includes sensitive data, you
may send it instead to genom...@soe.ucsc.edu.

Christopher Lee
UCSC Genomics Institute

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