I have a small set of avian RNA-seq data. As the first attempt, I mapped one FASTQ file using the latest GMAP to the same genome. Coverage is very low (I started with ca 35k sequences), and some unspliced mappings look doubtful. Hence my questions:
- Are there any other spliced mappers I should try, for both same species / different species (RNA-genome) mappings?
- Since I am searching for novel genes / splice forms, does it make sense to try error correction prior to mapping?
- Any program/pipeline to improve the 454 using Illumina RNA-seq?
Many thanks for your help