problem with retrieve mRNA (Transcript) sequence using local mirror

[Fu weiwei]

Dear UCSC Genome Browser Team,

I have built an UCSC local mirror. Now I have a gff3 annotation file and finally transformed it into bigbed format. Then I display gene annotation track like the picture below.  If I want to retrieve mRNA (Transcript) sequence instead of DNA sequence, what additional configuration should I do ?  

Waiting for your reply! Thank you very much for your time.

All the best,

Weiwei Fu

[Jairo Navarro Gonzalez]

Hello Weiwei,

Thank you for using the UCSC Genome Browser and your inquiry.

If you would like to obtain the predicted mRNA transcript, you will have to convert your GFF file into a bigGenePred file. For example, you can load the following bigGenePred hub that gives an option to get the predicted mRNA sequence using the reference genome sequence and the annotation:

http://genome.ucsc.edu/cgi-bin/hgc?db=hg38&c=chr1&l=11102836&r=11267747&o=11106534&t=11262507&g=hub_180419_bigGenePred2&i=ENST00000361445.5

You can learn more about the bigGenePred format from the following help pages:

http://genome.ucsc.edu/FAQ/FAQformat#format9.1
http://genome.ucsc.edu/goldenPath/help/bigGenePred.html

As for converting your GTF3/GFF to genePred, and then finally bigGenePred, you can use our conversion utilities. Start by selecting your operating-system specific utilities at our utilities downloads, and then select the utility you would like to use: gff3ToGenePred and genePredToBigGenePred.

For more information about these conversions, see our gff/gtf wiki page:

http://genomewiki.cse.ucsc.edu/index.php/Genes_in_gtf_or_gff_format#The_opposite_direction.2C_GTF_to_GenePred

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.

Jairo Navarro 
UCSC Genomics Institute

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