Reg: Help for data extraction from Genome Browser

Amit Jaiswal

unread,

Jul 9, 2021, 1:24:49 PM7/9/21

to gen...@soe.ucsc.edu

Dear Sir/Madam,

Hope you are doing well. I would like to seek your help regarding extracting corresponding information from gene names. I have around 100 genes of interest and I would like to extract the data such as RNA-seq results, CNV results, SNP results, DNA methylation of various cancers from Genome Browser. Is it possible to extract these information from different types of cancer related to my genes of interest? It would be great if you can suggest me in proceeding ahead. Please let me know if you need any other information and thanks for your valuable time.

With kind regards,

Amit Jaiswal

--

Yours Sincerely,

Amit Jaiswal

PhD / Graduate Student,

FSU, Jena, Germany &

HZNU, Hangzhou, China.

Matthew Speir

unread,

Jul 15, 2021, 6:42:34 PM7/15/21

to Amit Jaiswal, gen...@soe.ucsc.edu

Hello, Amit.

Thank you for your question about accessing data in the UCSC Genome Browser.

I would recommend exploring the data available in the Genome Browser to find the tracks that contain the data that you are interested in. Once you've identified these tracks, you can use the Table Browser to download the data for them. If you have the genomic positions of your genes (e.g chrX:151,283,001-151,290,000), you can use the Table Browser's "define regions" option to specify them. Here are some video tutorials that may be of interest to you:

How do I find all the SNPs in a gene using the UCSC Genome Browser? - directly relevant to your question about getting the SNPs in a gene. Getting data for other formats is just a matter of choosing a different output track/table.
How do I get the coordinates and sequences of exons using the UCSC Genome Browser? - while it discusses getting exon coordinates, getting transcript coordinates is just a matter of outputting an entry per whole gene rather than per exon.
How do I learn which tables belong to a data track on the UCSC Genome Browser? - will help you ensure you're choosing the right tables when outputting data from the Table Browser.

The Data Integrator may also be of interest to you. It allows you to intersect up to five tracks from the Genome Browser and output arbitrary columns from each of the tracks. This video explains how to use the Data Integrator: https://youtu.be/8ATcoDTOc0g. This answer to an old mailing list question may also provide some help with using the Data Integrator to extract data as well.

If you're new to using the Genome Browser, these three videos should give you a good introduction to using it and navigating around:

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.

Training videos & resources: http://genome.ucsc.edu/training/index.html

Want to share the Browser with colleagues? Host a workshop: http://bit.ly/ucscTraining

---

Matthew Speir

UCSC Cell Browser, Quality Assurance and Data Wrangler

Human Cell Atlas, User Experience Researcher

UCSC Genome Browser, User Support

UC Santa Cruz Genomics Institute

Revealing life’s code.

--

---
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 view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/105341625823053%40mail.yandex.com.

Amit Jaiswal

unread,

Jul 19, 2021, 12:45:02 PM7/19/21

to Matthew Speir, gen...@soe.ucsc.edu

Dear Dr. Speir,

Many thanks for your suggestions. I will have a try to your suggestions. If I come across any problems I will let you know. Thanks for your time.

With kind regards,

Amit Jaiswal

16.07.2021, 06:42, "Matthew Speir" <msp...@ucsc.edu>:

Reply all

Reply to author

Forward