Gbrowse and blast datasets

Gbrowse tracks

Details of tracks currently loaded onto GBrowse.

Version 5 Transcriptome and Version 0.5 Genome Assemblies

Putative gene models - The transcriptome assembly was mapped to the genome assembly using the software, GMAP, to generate putative gene models. Models are available for the full transcriptome (primary and alternate transcripts) or for primary transcripts. See Sequencing Strategy for details about the v5 transcriptome assembly. Transcript IDs have the following convention: version-ID (e.g. Nbv5tr5753726 is version Nbv5 transcriptome and ID of 5753726).

RNAseq expression profile - RNAseq read expression profile on the genome from 10 tissues are shown. Reads were aligned to the genome assembly using the TopHat2 package (bowtie2 aligner). Read depths were normalized to the total mappable reads per tissue, and multiplied by 1 million. Sample profiles can be over-layed (and auto-scaled) by clicking on 'Showing X of 10 tracks', and checking 'Semi-transparent overlap' at the bottom left corner. Tissues are Apex, Capsule, Drought stressed leaves, Flower, Leaf, Roots, Seedling, Stem, Tissue Culture and Whole plant.

Junctions - Intron/Exon junctions identified from RNAseq reads by TopHat2. Junctions can be view on a per-tissue basis on separate tracks or on one tract.

Single/Paired end RNAseq reads - Tracks showing the TopHat2 (bowtie2) alignment of individual RNAseq reads onto the genome assembly. These are combined reads from all the tissue libraries. Paired end tracks display mate information of the single end read data.

Coverage - Read depth profile from all RNAseq libraries (10 tissues) from the TopHat2 alignment. Red regions indicate depth below 20 reads, blue regions indicates depth above 20 reads.

Version 3 Transcriptome and Version 0.2/0.3 Genome Assemblies

Putative gene models - The transcriptome assembly was mapped to the genome assembly using the software, GMAP, to generate putative gene models. Transcript IDs have the following convention: version-kmer-ID (e.g. Nbv3K605753726 is version Nbv3, kmer of 60, and ID of 5753726).

Transcriptome profile - RNAseq read distribution profile from 12 different samples are shown. Reads were aligned to the genome assembly using the software, RSEM. Read depth at a position were normalized to the post-processed library size, and multiplied by 10 million. Sample profiles can be over-layed (and auto-scaled) by clicking on 'Showing X of 12 tracks', and checking 'Semi-transparent overlap' at the bottom left corner. Symbols: L - Lab line, QLD - Queensland line, WA - Western Australia line. Sample names are self explanatory, except for: Dstress - drought stressed leaves , Caps - capsules, T_C - tissue cultures of callus.

miRNAs - Small RNA reads from leaf samples were analyzed by the software, miRCAT from the UEA sRNA workbench.

Single/Paired end RNAseq reads - Tracks showing the RSEM alignment of individual RNAseq reads onto the transcriptome assembly. These are combined reads from all the 'L' RNAseq samples, used also for the transcriptome assembly. Paired end tracks display mate information of the single end read data.

Coverage - Read depth profile of all 'L' RNAseq samples combined (from RSEM alignment). Red regions indicate depth below 20 reads, blue regions indicates depth above 20 reads.

Blast databases

For details about these assemblies, see Sequencing Strategy.

Genome assembly - There are currently two formats of the assembly: scaff+contigs - contigs that are scaffolded by paired-end/mate-pair information, containing N's for yet unresolved gaps; contigs - scaffolds are split into individual contigs, removing N's. The current assembly (v0.3) scaffold IDs have the following convention: version-scaffoldID (e.g. Nbv0.3scaffold18718 is version Nbv0.3, and ID of scaffold18718).

Transcriptome assembly - Blast-like descriptions of contigs were added by an in-house annotation pipeline at the PFR institute. Transcript IDs have the following convention: version-kmer-ID (e.g. Nbv3K605753726 is version Nbv3, kmer of 60, and ID of 5753726).

Software and tools references