Detection Of Alternative Splicing And Gene Fusion Without Genome Info

Question

[Dejian]

RNA-seq data can be used to detect alternative splicing and gene fusion, which will be relatively easy if genome sequences are available. What if the genome information is not available? Are there some examples or tools to do these two analysis without genome information?

Answer 1

[brentp]

I haven't used it, but just saw this come out: Full-length transcriptome assembly from RNA-Seq data without a reference genome, from the Broad Institute.

Available from sourceforge here.

EDIT:

It seems that (also recently published) NSMAP does not need a reference genome either.

[Dejian]

Thank you, brentp. NSMAP seems to be what I need. Hope it helps.

Answer 2

[madk00k]

Most commonly used tools are

• Trans-ABySS
• Trinity
• Oases (based on Velvet, combines ideas from the two above)