extracting intron coordinates with refseq gene names

[VG]

Hi,

I am trying to use table browser for hg19 and hg38 genome assembly and want to get all the intron coordinates of the genome but with Refseq names of the genes and not only NM_ NR_ etc names.

How can I do this?

Regards

Varun

[Jairo Navarro Gonzalez]

Hello Varun,

Thank you for using the UCSC Genome Browser and your inquiry.

You may be interested in the refFlat table, which contains both the gene name (usually a HUGO Gene Nomenclature Committee ID) and its accession number. If you select the refFlat table on the Table Browser, you can get of all the introns in the RefSeq gene set. You can follow these steps to get these intronic regions with RefSeq names for hg19 and hg38:

Step 1: Configure the Table Browser

Navigate to the Table Browser and apply the following settings:

clade: mammal
genome: Human
assembly: Dec. 2013 (GRCh38/hg38)
group: All Tables
database: hg38
table: refFlat
region: genome
output format: BED - browser extensible data

Once you have applied the following settings, click get output.

Step 2: Get introns in BED format

After clicking get output, you will be taken to a new page where you can create one BED record per intron. 
After selecting Intron Plus, click get BED.

You may notice duplicate entries in the output and may be the result of alternatively spliced transcripts. Here is a previously answered question that may help in removing these duplicate items.

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.

Jairo Navarro 
UCSC Genomics Institute

--

---
You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Public Support" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genome+un...@soe.ucsc.edu.
To post to this group, send email to gen...@soe.ucsc.edu.
Visit this group at https://groups.google.com/a/soe.ucsc.edu/group/genome/.
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CAN7A_Qzj0POxfBfyPuRQ0%2BChhxJnRUPVr_wyjfOjJfxkopBWqg%40mail.gmail.com.
For more options, visit https://groups.google.com/a/soe.ucsc.edu/d/optout.