Why genomic information shown in UCSC/Ensembl browser for a specific gene is different from it's bed file?

Question

[bioinf_data-analyst9449]

I have a specific gene, assume name "gen1". I want to find in which chromosome it is and it's positions. I queried the same using UCSC Browser and Ensembl, and got the output. Now, I have to download the same genetic information of that gene in bed format.

In bed format, one and more nu. of chromoses are available with their start and end positions.

Why it is in such format, in browser it displayed one chromosome but in bed file, nu. of chromosomes are available.

FYI: I am a bioinformatician and new to the field Human Genetics and NGS.

Pls guide. !!

thanks.

[Denise CS]

Can you give us some examples of genes whose coordinates from the bed file don't match what you see on the UCSC and Ensembl browsers? Things to double check: same assembly, same version of the GENCODE gene set, whether you are dealing with the 'canonical' (whatever that means) or longest transcript, if the CDS is the only bit provided (rather than the UTRs), etc...

Answer 1

[genecats.ucsc]

Our data tables store data for each transcript (one row per transcript generally), and since multiple transcripts can be associated with the same gene symbol, when you download data for a particular gene symbol, you will get all of the transcripts associated with that gene symbol, and not just one. You may also see transcripts that map to alternative haplotype sequences.

That being said, if you could share an example search, I can give you more information on what exactly you are seeing.

If you have further questions about the UCSC Genome Browser or our utilites or data, feel free to send an email to one of mailing lists below:

• [e-mail] for general questions (public list)
• [e-mail] for question concerning private data (private list)
• [e-mail] for questions concerning the setup and running of your own UCSC Genome Browser installation

ChrisL from the UCSC Genome Browser