Question: Retrieving Basewise Phylop Scores?!?
gravatar for Morteza
4.7 years ago by
Morteza0 wrote:

Is there any way for batch retrieving per base phyloP scores for hg19 and mm10 from UCSC (or other places if exists).

I have a large list of coordination and positions in several chromosomes and I'm trying to find a fast and programmatical way to get the base-wise phyloP scores for them.

I tried following methods;

1) Querying from "Table Browser" for each positions.
This method is not reasonable and will take a long time.

2) Downloading FixWig flat files from FTP.
The file size will be too big after preparation for lookup and conversion process will take considerable time.
phyloP files for hg19 have more than 5Gig size and after converting them to "Bed" and creating "database" (eg. Sqlite, for fast look up), final size will exceeds of 150G (and need several days time on my labtop, I tried it and then skipped it after 24 hours)

3) Querying from mysql command line.
The mysql only has access to the "Annotation Database" and for phyloP only return to me "bin data" , not per base scores (from "phyloP100wayAll" table).

4) Using Bioconductor package "rtracklayer"
The "rtracklayer" is great, but unfortunately has not batch capability, is very very slow and confusing when encounters connection problem (or server load).

5) Using DAS server.
To my knowledge DAS has not this capability.

In addition, I find "ruby-ucsc-api" and "batchUCSC" perl script. But, both work based on mysql interface and have same problem.

I will be grateful for any help.

ucsc conservation score api • 1.6k views
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