retrieve RNA exon/intron sequence info from coordinates
Stephen Meltzer
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
Matthew Speir
Thank you for your question about obtaining sequence using the UCSC Genome Browser.
Could you provide more details as to what information you're looking to obtain? Are you looking for the genomic sequence of the coordinates you provided? Or something else?
Additionally, could you provide the assembly that you're working with (e.g. hg19, hg38, or mm10)?
I hope this is helpful. 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 Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Matthew Speir
UCSC Genome Bioinformatics Group
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Stephen Meltzer
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
Matthew Speir
Thank you for providing more details.
You can get the sequences of the regions from the file you attached to your original message using a BED6 custom track and the Table Browser.
A. Create a BED6 file
You can find more information on the BED format here: https://genome.ucsc.edu/FAQ/FAQformat.html#format1
The first six columns are:
1. Chromosome name
2. Chromosome start position (0-based, more here: http://genome.ucsc.edu/blog/the-ucsc-genome-browser-coordinate-counting-systems/)
3. Chromosome end position (1-based)
4. Item name
5. Score (number between 0-1000, not important for your case, but needs to be filled in)
6. Strand
Example of creating a BED6 line out of the first region in your file:
chr6 108663453 108664889 region1 1000 +
You will need to create a BED line such as this for every region you want output for.
B. Upload BED6 file as a custom track
After you've created your BED6 file of regions, you will need to upload it as a custom track:
https://genome.ucsc.edu/cgi-bin/hgCustom
You can paste the contents of your BED6 file into the box below "Paste URLs or data", or you can upload the file
from your computer using the "Choose File" button. Then click "Submit".
After upload, select "Table Browser" from the drop-down and click "Go".
C. Use the Table Browser to get sequence for your custom track
Make the following selections on the Table Browser, https://genome.ucsc.edu/cgi-bin/hgTables:
clade: Mammal
genome: Human
assembly: Dec. 2013 (GRCh38/hg38)
group: Custom Tracks
track: Your_Track_Name
table: primary table for your track
region: genome
output format: sequence
output file: Enter a file name or leave blank to view results in the web browser
After making these selections, click "get output". On the next screen, select any sequence formatting options
you would like and then click "get sequence".
I hope this is helpful. 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 Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Matthew Speir
UCSC Genome Bioinformatics Group