write the query for bigbed and import gtf with gene sequence viewing

[weiweifu666]

Dear UCSC Genome Browser Team,
 

I have two questions about the trackDb settings. One is when I use the program hgBbiDbLinkload to load bigbed file into mysql, it only load the file path, I know it's right but if I want to type a search term such as gene name into the position box, How to write the query to realize this?  The second question is that I want to load gene annotation file gtf into tracks, I have to make a series of transformation and finally generated the bigbed files. So, is there a simple way to import GTF files directly? Addtionally, when I click the gene structure figure in the track, can I view the gene sequence (fasta format) and exon information? How should I configure it?

Thank you very much for your time.

Kind regards,

Weiwei fu

 

[Matthew Speir]

Hi Weiwei,

Thank you for your question about creating tracks in the UCSC Genome Browser.

For your first question of how to enable searching for your bigBed tracks please see the following answers to previous mailing list questions:
https://groups.google.com/a/soe.ucsc.edu/forum/#!msg/genome-mirror/loZy2Ps7sDU/fMiK_1ZaEQAJ
https://groups.google.com/a/soe.ucsc.edu/forum/#!msg/genome/1dG6Wi1htFk/x4CchNTcmsQJ
https://groups.google.com/a/soe.ucsc.edu/forum/#!msg/genome/x26OjYKCRAo/soImKyEZrt8J

For your second question of creating tracks out of your GTF files, you will need to convert your files to bigGenePred files to create Genome Browser tracks from them. You will need to first convert your files from GTF into genePred format. This can be done using our "gtfToGenePred" utility that can be downloaded from our downloads server here: http://hgdownload.soe.ucsc.edu/admin/exe/. Next you can follow the instructions on the bigGenePred format help page to convert this genePred file into a bigGenePred file: https://genome.ucsc.edu/goldenPath/help/bigGenePred.html. You should be able to use the same steps you've been using to load your bigBed files into your mirror to load these bigGenePred files. You can also see the trackDb settings available to bigGenePred tracks here: https://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html#bigGenePred_-_Gene_Annotations.

I hope this is helpful. 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 Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group

--

---
You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Public Support" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genome+un...@soe.ucsc.edu.
To post to this group, send email to gen...@soe.ucsc.edu.
Visit this group at https://groups.google.com/a/soe.ucsc.edu/group/genome/.
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/50990d4b.9842.15c4a89e756.Coremail.weiweifu666%40126.com.
For more options, visit https://groups.google.com/a/soe.ucsc.edu/d/optout.