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
1 answer
TopHat2 is good for reference alignment. You could try Dissect tool too.
If you are trying to look into the novel forms why don't you try for denovo assembly with Rnnotator, SOAP or Trinity. Then by mapping these generated contigs to your reference you might be able to know more about the alternative splicing.
Before alignment or assembly try for the Quality filtering with FastQC, NGSQC, NGSUtils. Sickle or Trimmomatic too might help but I never used them.
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