Difference between USCS exon coordinates and ensembl

Question

[amy__]

Hello,

I am trying to extract the coordinates for the exons in numerous genes.

For example, APC using the MANE transcript: NM_000038.6

When downloading the USCS table browser for just exons from HG38 I get these coordinates for the exons (example exon 1):

chr5 112737884 112737925

However, when I look on ensembl https://www.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000134982;r=5:112707498-112846239;t=ENST00000257430 the coordinates are one base off - does anyone know why or which coordinates I should use?

chr5 112737885 112737925

Thanks! Amy

[ATpoint]

What did you download from UCSC? 1-off usually means one file is zero-based and the other 1-based. BED files from UCSC are 0-based, Ensembl viewers are 1-based.

[amy__]

Hi ATpoint,

I went to http://genome.ucsc.edu/cgi-bin/hgTables and did:

1. 

then:

1. 

Then searched the downloaded file for NM_000038.6

Which shows:

[ATpoint]

Yes, BED file, so this is zero-based and on Ensembl Viewer it is 1-based. So that is the reason.

[amy__]

Great thank you, I want to use the coordinates in bedtools to work out the coverage of some genes over those regions - do you think use the UCSC 0-based coordinates? Thanks! Amy