RefSeq or GENCODE

[Gmail Marcin]

Hi,
I have RRBS question related specifically to the annotation strategy.  So I am contemplating to switch from RefSeq to GENCODE  (humans) as a source of annotation and I would like to hear people thoughts about it. For RRBS I think Gencode should be better, as what we are looking for are also regions between genes (intragenic regions).

(Further reading about RefSeq vs GENCODE here http://iobio.io/2016/03/21/gene-sets/ )

http://www.gencodegenes.org/releases/current.html
I was adviced to use  Basic gene annotation but I do not see the info about introns. What do I miss compared to RefSeq protocol taken from here:

http://zvfak.blogspot.no/2012/09/downloading-annotation-files-for.html

Many thanks,

Marcin

[Altuna Akalin]

I think gencode is better, used to be more complete but refseq might have caught up. You can download gencode bed files from UCSC, GFF/GTF to bed conversion might be problematic. 

Best,

Altuna

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[Gmail Marcin]

Thank you Altuna. If someone else has some experience in comparing both, it would be great to hear. Especially for the regions between genes.

Thinking about it the intragenic regions, is there any way to twist the readTranscriptFeatures function so it also gives this information and not only introns, exons, promotor regions and TSS?

Many thanks,

Marcin

On 8 June 2017 at 18:14, Altuna Akalin <aak...@gmail.com> wrote:

I think gencode is better, used to be more complete but refseq might have caught up. You can download gencode bed files from UCSC, GFF/GTF to bed conversion might be problematic. 

Best,

Altuna

On Thu, Jun 8, 2017 at 3:39 PM, Gmail Marcin <marcin.b...@gmail.com> wrote:

Hi,
I have RRBS question related specifically to the annotation strategy.  So I am contemplating to switch from RefSeq to GENCODE  (humans) as a source of annotation and I would like to hear people thoughts about it. For RRBS I think Gencode should be better, as what we are looking for are also regions between genes (intragenic regions).

(Further reading about RefSeq vs GENCODE here http://iobio.io/2016/03/21/gene-sets/ )

http://www.gencodegenes.org/releases/current.html
I was adviced to use  Basic gene annotation but I do not see the info about introns. What do I miss compared to RefSeq protocol taken from here:

http://zvfak.blogspot.no/2012/09/downloading-annotation-files-for.html

Many thanks,

Marcin

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[Altuna Akalin]

you can read the bed12 file as a regular bed file (genomation::readBed), just containing start-end positions of the genes. Then, you have to use GenomicRanges functions to I thinks it is called "gaps" or "gap" or something like that to get the regions between genes. But some genes are very long, maybe you want to filter genes based on evidence or protein coding capacity. 

Best,

Altuna

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[Gmail Marcin]

I see, I found also this: https://stackoverflow.com/questions/29253412/finding-intergenic-regions   if someone would need a detailed recipe so similar can be done on UCMC Gencode table.  They reduce also + - to *.

Many thanks,

Marcin

[Kristina Santucci]

Hi Altuna,

Could you point me into the right direction to get the bed12 file for Gencode v49 GRCh38? I can't seem to find this and I'm hoping to avoid any manual conversions.

Thank you in advanced!

Cheers,

Kristina.

On Friday, June 9, 2017 at 2:15:16 AM UTC+10 Altuna Akalin wrote:

I think gencode is better, used to be more complete but refseq might have caught up. You can download gencode bed files from UCSC, GFF/GTF to bed conversion might be problematic. 

Best,

Altuna

On Thu, Jun 8, 2017 at 3:39 PM, Gmail Marcin <marcin.b...@gmail.com> wrote:

Hi,
I have RRBS question related specifically to the annotation strategy.  So I am contemplating to switch from RefSeq to GENCODE  (humans) as a source of annotation and I would like to hear people thoughts about it. For RRBS I think Gencode should be better, as what we are looking for are also regions between genes (intragenic regions).

(Further reading about RefSeq vs GENCODE here http://iobio.io/2016/03/21/gene-sets/ )

http://www.gencodegenes.org/releases/current.html
I was adviced to use  Basic gene annotation but I do not see the info about introns. What do I miss compared to RefSeq protocol taken from here:

http://zvfak.blogspot.no/2012/09/downloading-annotation-files-for.html

Many thanks,

Marcin

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[alex....@gmail.com]

Hi Kristina,

You can follow the original instructions from Altuna: https://zvfak.blogspot.com/2012/09/downloading-annotation-files-for.html 
Conversions are usually necessary if you have specific requirements or use a less well-annotated organism. 

Best,

Alex