Question: How to collect the phastCons and phyloP data from Ensembl
0
gravatar for wangdp123
23 months ago by
wangdp123250
Oxford
wangdp123250 wrote:

Hi there,

Does anybody know if Ensembl/Ensemblgenomes provides the data of sequence conservation scores (e.g., phastCons, phyloP) for each nucleotide of the genomes? If so, where to download the data?

Many thanks,

Tom

phylop phastcons ensembl • 1.1k views
ADD COMMENTlink modified 23 months ago by Emily_Ensembl21k • written 23 months ago by wangdp123250

wangdp123 : Don't forget to follow up on your threads.

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one if they work.
Upvote|Bookmark|Accept

Please do the same for your previous posts as well.

ADD REPLYlink modified 23 months ago • written 23 months ago by GenoMax95k
5
gravatar for Emily_Ensembl
23 months ago by
Emily_Ensembl21k
EMBL-EBI
Emily_Ensembl21k wrote:

GERP conservation scores here.

ADD COMMENTlink written 23 months ago by Emily_Ensembl21k

Thanks Emily. Are there any conservation scores for Ensemblgenomes database (http://ensemblgenomes.org/) such as Ensembl Fungi, Ensembl Plants, Ensembl Protists and Ensembl Metazoa?

ADD REPLYlink written 23 months ago by wangdp123250

No, we did not do multiple alignments for them.

ADD REPLYlink written 23 months ago by Emily_Ensembl21k
2
gravatar for Santosh Anand
23 months ago by
Santosh Anand5.2k
Santosh Anand5.2k wrote:

You may easily get them from UCSC (Google it). The reference genome assembly doesn't change between different sites - so it will give the same info.

ADD COMMENTlink written 23 months ago by Santosh Anand5.2k
1

Indeed, link for hg38: http://hgdownload.cse.ucsc.edu/goldenpath/hg38/

ADD REPLYlink written 23 months ago by Kevin Blighe69k

Thanks. Any idea about how to get the conservation scores for each gene or exon by making use of the single nucleotide data? I know that the bigwig files contain the conservation score for each nucleotide. Should we use the sum or mean to calculate the scores for single gene or exon?

ADD REPLYlink written 23 months ago by wangdp123250

That is a design choice that you should make. For me, calculating mean per sliding window interval makes sense.

ADD REPLYlink written 23 months ago by Kevin Blighe69k
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