New & Noteworthy

Explore the S288C Transcriptome in JBrowse

April 25, 2019

We have recently equipped our genome browsing tool JBrowse with 9 new Transcriptome data tracks, making JBrowse an even more powerful way to explore the vast heterogeneity of the S288C transcriptome. These information-rich data tracks visualize RNA transcripts from the TIF-seq dataset published by Pelechano et al. (2013), enabling quick and easy viewing of the position, length, and abundance of transcript isoforms sequenced in the study.

You can easily access these new tracks by entering JBrowse and clicking on the left-hand “Select tracks” tab. They are located in the Transcriptome category. In addition to viewing the data in JBrowse, you can also download the .gff3 and .bw files for these tracks for use in your own analyses.

Check out our video tutorial from the SGD YouTube channel at the top of this page for a quick overview of the new transcriptome data tracks and how to access them. More information about these tracks and how SGD created them can also be found on our Genome Browser help page.

If you have any questions or feedback about the new Transcriptome data tracks or about our genome browser, please don’t hesitate to contact us.

Data tracks that visualize transcript isoforms that fully overlap a gene coding region:

Data Track Title Description
longest_full-ORF_transcripts_ypd This track contains the longest transcript overlapping each individual ORF completely for WT cells grown in glucose (ypd) media.
longest_full-ORF_transcripts_gal This track contains the longest transcript overlapping each individual ORF completely for WT cells grown in galactose (gal) media.
most_abundant_full-ORF_transcripts_ypd This track contains the most abundant transcript overlapping each individual ORF completely for WT cells grown in glucose (ypd) media.
most_abundant_full-ORF_transcripts_gal This track contains the most abundant transcript overlapping each individual ORF completely for WT cells grown in galactose (gal) media.
unfiltered_full-ORF_transcripts This track contains all transcripts that overlapped individual open reading frame (ORF) completely for WT cells grown in either glucose (ypd) or galactose (gal) media.

Data tracks that quantify the number of transcripts that cover a given nucleotide in the S288c genome:

Data Track Title Description
plus_strand_coverage_ypd For WT cells grown in glucose media (ypd), the amount of transcripts covering each position on the plus strand is represented in this track.
plus_strand_coverage_gal For WT cells grown in galactose media (gal), the amount of transcripts covering each position on the plus strand is represented in this track.
minus_strand_coverage_ypd For WT cells grown in glucose media (ypd), the amount of transcripts covering each position on the minus strand is represented in this track.
minus_strand_coverage_gal For WT cells grown in galactose media (gal), the amount of transcripts covering each position on the minus strand is represented in this track.

 

Categories: Tutorial New Data