Dear Genome:
I have the attached set of coordinates but am unable to retrieve their corresponding exact RNA (exon and intron) sequences.
I need these coordinates to be carried into the RNA sequence data.
I do not just want to pull the entire gene or cDNA.
How can I do this?
Stephen J. Meltzer, M.D.
American Cancer Society Clinical Research Professor
The Harry & Betty Myerberg/Thomas R. Hendrix Professor of Gastroenterology
Departments of Medicine and Oncology
The Johns Hopkins University School of Medicine & Sidney Kimmel Comprehensive Cancer Center
1503 E. Jefferson Street, Room 112
Baltimore, MD 21287
410-502-6761 Lisa Gaines-Thomas
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Dear Matthew,
Thank you for your reply! We are trying to generate putative circular RNA sequences.
All we have are the start and end coordinates of each potential circular RNA.
We would like to actually pull the RNA sequence between the two coordinates for each circular RNA.
That way, we can predict the complete sequences and sizes of the circular RNAs.
We also (crucially) need exon and intron information.
We are assuming the circular RNAs contain only exonic RNA.
Steve