12 Nov 18:22 2015
Digest for genome <at> soe.ucsc.edu - 5 updates in 5 topics
<genome <at> soe.ucsc.edu>
2015-11-12 17:22:11 GMT
2015-11-12 17:22:11 GMT
- Queries regarding axtChain and netToAxt - 1 Update
- Custom BED track itemRgb alpha value - 1 Update
- canFam3.1 EnsembGeneID to GeneName - 1 Update
- rmsk table data nature information - 1 Update
- find promoter sequences of genes in Pichia pastoris - 1 Update
"Rohit Kolora" <rohit <at> bioinf.uni-leipzig.de>: Nov 12 02:14PM +0100
Dear UCSC developers,
I have a few questions regarding the UCSC tools for chain building and
netting from axt alignments.
1) blocks after duplicate removal
"12 blocks after duplicate removal" - During axtChain option, there is a
process of removing the duplicates. What kind of duplicates do you refer
to? Is it query wise duplicate i.e. hits that are covered by the same
query at multiple places (or) target-related i.e. region of target that is
covered by multiple queries?
How will a region be extended if they are covered by both strands, one
strand by a gap and other strand due to an exact hit, are they both
mentioned as different chains?
2) noSplit option in netToAxt
"Don't split chain when there is an insertion of another chain" - Does
this mean that a particular target sequence when being chained with one
query is split at a point since the target-region has a hit with another
If so, is there an option to net this region but still have information
regarding these overlaps.
Chris Cheshire <chris.j.cheshire <at> gmail.com>: Nov 12 09:45AM
I am in the process of creating some custom tracks and I would like to
represent score on a coloured element. Currently, I have one greyscale
track for strength and another identical track to indicate colour. Ideally
I would like to combine the two and have the score fade the alpha value of
the colour up and down. Is this possible? I have search the documentation
but I cannot see how to do this...
Chris Cheshire (UCL)
"Arumilli, Meharji" <meharji.arumilli <at> helsinki.fi>: Nov 12 11:36AM +0200
We are trying to convert Ensembl Gene ID's to corresponding Gene Name
The UCSC table for the "ensGene" track has the gene IDs and the
transcript IDs but not the gene names.
And "ensemblToGeneName" table has the transcript ID with gene name.
Would you help us how to match the Gene ID's retrieved from UCSC browser
with the gene names?
aboucheha <at> ibisc.univ-evry.fr: Nov 11 11:02AM +0100
i have a question about transposons downloaded from rmsk table for human,
mouse and Drosophila melanogaster species, if they are experimentally
validated in nature or predicted
thank you in advance
Haitian Liu <hliu <at> scripps.edu>: Nov 11 10:40AM -0800
I would like to use your database to search promoter sequences with genes in Pichia pastoris. When I use Blat and enter the organism, I can't find Pichia pastoris. So which genome I should use for the search? If no Pichia pastoris genome is available, how will I perform the search? Any suggestions? Many thanks!