Question: How Do You Manage Moving Existing Projects To A New Genome Build?
7
gravatar for Casbon
7.6 years ago by
Casbon3.1k
Casbon3.1k wrote:

If you have a set of coordinates to a specific genome build, are there any decent tools/approaches for porting those coordinates to a new build?

genome • 3.3k views
ADD COMMENTlink modified 6.7 years ago by Pierre Lindenbaum100k • written 7.6 years ago by Casbon3.1k

This post details various options for coordinate conversions between builds: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)

ADD REPLYlink written 10 weeks ago by Malachi Griffith16k
8
gravatar for Daniel Swan
7.6 years ago by
Daniel Swan13k
Aberdeen, UK
Daniel Swan13k wrote:

For UCSC data just follow the suggestions here:

http://genome.ucsc.edu/FAQ/FAQdownloads.html#download28

Although to be honest it seems more common to just stick to one assembly for the duration of the work (yes that is anecdotal experience) but if you always reference the build you use throughout the data release and publication process I don't see this being a problem (of course YMMV if what you are working on varies greatly between builds).

ADD COMMENTlink written 7.6 years ago by Daniel Swan13k
4

I'd also recommend sticking with one build whenever possible, simply because the alternatives are just too horrible.

ADD REPLYlink written 7.6 years ago by Neilfws47k

Is there really nothing better than blatting against the new genome?

Given ensembl tracks the sequences based on the assembly I would hope you could follow changes in the assembly.

ADD REPLYlink written 7.6 years ago by Casbon3.1k
7
gravatar for Pierre Lindenbaum
7.6 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum100k wrote:

Use LiftOver http://genome.ucsc.edu/cgi-bin/hgLiftOver

I also remember that I used the mapping information of dbsNP or UniSTS for both build to find how a genomic segment 'moved'.

Moreover, if you store this information in a DB, or in any file, always include a column for the build or else your data will be a mess when you later have a look at it.

Pierre

ADD COMMENTlink written 7.6 years ago by Pierre Lindenbaum100k

The galaxy platform http://main.g2.bx.psu.edu/ integrates LiftOver and it is excellent for working with coordinate based data: not least because the data itself can be assigned species and build information in the metadata.

ADD REPLYlink written 7.1 years ago by Alastair Kerr5.2k
4
gravatar for Pierre Lindenbaum
7.1 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum100k wrote:

A new NCBI service was announced today: "NCBI Genome Remapping Service"

http://www.ncbi.nlm.nih.gov/genome/tools/remap

ADD COMMENTlink written 7.1 years ago by Pierre Lindenbaum100k

cool. idea on how that might be implemented? any public softwares?

ADD REPLYlink written 7.1 years ago by Haibao Tang2.9k

I was just going to mention that! Here's the tweet if anyone wants to re-tweet it: http://twitter.com/NCBI/statuses/26097191403

ADD REPLYlink written 7.1 years ago by Mary11k
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