Question: download recent list of human exons
0
gravatar for Maria333
2.4 years ago by
Maria33310
European Union
Maria33310 wrote:

Hi,

Does anyone know where to download the most recent list of human exons? The most recent I can find is from the 1000G and from 2012.. 

Thank you

human exons • 794 views
ADD COMMENTlink modified 2.4 years ago by Giovanni M Dall'Olio25k • written 2.4 years ago by Maria33310
2

This question is not very clear...  To my knowledge 1000G (i.e. the 1000 genomes project) is not really a source of exon annotations.  Human exon annotations can be obtained from quite a few sources.  Two of the most popular are Ensembl and UCSC.  Can you elaborate a bit more on your question though, in particular what your goals are?

ADD REPLYlink written 2.4 years ago by Malachi Griffith16k

Hi Malachi,

Thanks for your response. I need to have the exact coordinates of the human exons. The latest one is located in the 1000 Genomes project website and it is from 2012.. Hope it is more clear now..  

ADD REPLYlink written 2.4 years ago by Maria33310
1

There are definitely GENCODE updates more recent than 2012. As Devon posted below, you'll want a GTF file from one of the sources he listed. You can also use the UCSC table browser function to generate these sorts of files from whichever data source you chose (UCSC, Ensembl, GENCODE). They will essentially be quite similar regardless of source.

ADD REPLYlink written 2.4 years ago by Dan Gaston6.9k
2

Either download a GTF file for Ensembl/UCSC/Gencode (they'll essentially be identical for humans) or use biomart.

ADD REPLYlink written 2.4 years ago by Devon Ryan73k

What format do you need them in? Do you mean you need coordinates of all exons?

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by igor4.9k

I need them in a bed format and yes, I need the coordinates of all human exons.. I emailed 1000G but the latest version they have is from 2013 since they stopped doing sequencing.. 

ADD REPLYlink written 2.4 years ago by Maria33310

You can download GTF from Ensembl or UCSC. Then use something like gtf2bed (http://bedops.readthedocs.org/en/latest/content/reference/file-management/conversion/gtf2bed.html) to convert to BED.

ADD REPLYlink written 2.3 years ago by igor4.9k
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