#RNA SEQUENCE SERIES#

By default, the many tracks are displayed in the layered FlyBase “TopoView” format, and data are shown on a log2 scale, since they range over many orders of magnitude. Choose datasets for expression by stage, tissue, treatments, or cell lines. RNA Seq Part III: Searching for Similarly Expressed GenesįlyBase JBrowse has several tracks that display RNA-Seq expression profiles, which give coverage values base-by-base across the genome.RNA-Seq Part II: Using RNA-Seq Profile Search.RNA-Seq Part I: Using GBrowse - Warning: The GBrowse genome viewer has been updated to JBrowse, but techniques shown here are still useful in JBrowse.

#RNA SEQUENCE SERIES#

For purposes of presentation and queries, values were assigned to one of eight bins, from very low to extremely high.Ī series of video tutorials describing different RNA-Seq tools is available. For each modENCODE RNA-Seq sample, gene expression level was calculated as RPKM within the exonic extent of the gene, as described in Gelbart and Emmert, 2013. The RNA-Seq query tools are restricted to the modENCODE datasets. In GBrowse genomic views, several other RNA-Seq datasets are also presented. RNA-Seq reads were mapped to the Release 6 genome assembly as described in Brown et al., 2014.

The primary RNA-Seq data in FlyBase are the modENCODE data originally published in Graveley et al., 2011 and Brown et al., 2014, comprising 30 developmental stage expression profiles, 29 tissue expression profiles, 25 treatment/condition expression profiles and 24 cell line expression profiles.

Rna sequence