Adding track hubs to Ensembl Plants
(a) How many publicly available track hubs are there for the Solanum lycopersicum genome?
(b) Add the RNASeq-er alignment hub for ENA runs in ERP022223 track hub containing Illumina RNA-seq data of tomato roots colonized by the plant growth-promoting rhizobacterium Pseudomonas fluorescens strain CREA-C16. Search for Solyc07g065860.3, a tomato orthologue of the Arabidopsis RGI3 gene involved in regulation of root development root meristem growth. Is this gene expressed?
(c) Go to the region 7:67591664-67591688. Can you see any mismatches between reads and the reference assembly? Are they real SNPs or sequencing errors?
Go to Ensembl Plants and click on View full list of all species. Search the table for Solanum lycopersicum. Click on the species name to go to the species homepage.
Select Display your data in Ensembl Plants to get to the custom track menu, then click on Track Hub Registry Search in the side panel. Hit Search to find all available track hubs.
There are 315 track hubs currently available for tomato.
Click Search again at the top of the page and type ERP022223 in the provided text search box. Click Search, then Attach this hub in the search results and close the window by clicking on the tick. Search for Solyc07g065860.3 in the search box. Click on the location coordiantes to go to the Location tab.
This gene is expressed as indicated by the high coverage of RNAseq reads mapping to this locus.
From the region page, put the coordinates 7:67591664-67591688 into the Location box.
There are 11 mismatches between the reads and the genome assembly indicated in red. They represent sequencing errors, as they are found in single reads and concentrate around the read ends.