LRGs in the Genome Browser

[Jackie MacArthur]

Hi,

I work with Fiona Cunningham at the EBI on the LRG project. LRGs are now viewable in the genome browser if you search and view a gene with an associated LRG e.g. if you search for TP53 you can see LRG_321. However I couldn’t find a way to search for a particular LRG i.e. entering “LRG_321” in the “Search term” box. Is it possible to do this and if not would you be able to add this functionality?

Many thanks

Jackie

Jacqueline MacArthur PhD
European Bioinformatics Institute (EMBL-EBI)

[Steve Heitner]

Hello, Jackie.

We actually have an LRG Regions track in the Mapping and Sequencing group
and an LRG Transcripts track in the Genes and Gene Predictions group. The
LRG Regions track is bigBed-based and searching is not currently possible
within Browser bigBed tracks, though we are currently working to address
this. Searching is possible in the LRG Transcripts track, however. As you
noticed, searching "LRG_321" previously produced no results. The items in
the LRG Transcripts track have names like "LRG_321t5" which only came up
when you searched that term specifically. We just added new search rules
that will find all items in the LRG Transcripts track containing "LRG_321"
when searching by that term. I hope this is helpful.

Please contact us again at gen...@soe.ucsc.edu if you have any further
questions. All messages sent to that address are archived on a
publicly-accessible Google Groups forum. If your question includes
sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Steve Heitner
UCSC Genome Bioinformatics Group

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[Jackie MacArthur]

Hi Steve,

Many thanks for making that change. I will add an item to the LRG news page and mailing list to let our users know that this functionality is available.

Do you have a timescale for when the LRG genomic regions will be searchable?

Thanks

Jackie

Wellcome Trust Genome Campus
Hinxton
Cambridge, CB10 1SD

Phone: + 44 (0) 1223 49 4434
Email: ja...@ebi.ac.uk

[Brian Lee]

Dear Jackie,

Thank you for your message and sharing the update with your users. Unfortunately we do not have a time estimate of when the code will be changed and the new searching function will be available for the bigBed LRG genomic regions file formats at this time.

Thank you again for your using and helping us improve the UCSC Genome Browser by sharing your experience. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee

UCSC Genome Bioinformatics Group

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