About
Initial Goals of the Project
First Goal: Annotation Improvement.Collect RNA-seq data from multiple library preparaions, intended as as resource to faciitate in the annotation of existing NHP genomes as well as new or pending NHP genome projectes. For specific species we will:
- Map reads to reference, predict transcripts, compare to existing annotations
- Per-base BigWig files for easy browsing in a genome browser (such as UCSC or IGV)
- De novo assembly of left over reads, align assembled contigs to reference genome or use blast to NR; locate where gaps/errors are in published genome
We hope to partner with groups working on new NHP genomes, exploring methods where de novo transcript assembly can help in guiding genome assembly. Communicate with genome center and get the available draft genome assembly. Share the results with genome sequencing and publish together or as a companion.
Third Goal: From-Scratch Hybrid AssemblyIn contrast to the guided assembly, we are testing algorithms and methods for a de novo assembly using hybrid approaches (PacBio/ILMN, RNA/DNA).
Additional planned efforts
- Gene models for each tissue from each animal and corresponding isoform sequences
- Expression values for each annotated gene and exon
- Novel transcriptionally active regions (TARs) and their distance to nearest 5’ and 3’ gene
- Prediction of canonical and alternative usage exons