Question: Detection Of Alternative Splicing And Gene Fusion Without Genome Info
1
gravatar for Dejian
8.0 years ago by
Dejian1.3k
United States
Dejian1.3k wrote:

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?

gene splicing rna • 2.4k views
ADD COMMENTlink written 8.0 years ago by Dejian1.3k
2
gravatar for brentp
8.0 years ago by
brentp23k
Salt Lake City, UT
brentp23k wrote:

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.

ADD COMMENTlink written 8.0 years ago by brentp23k

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

ADD REPLYlink written 8.0 years ago by Dejian1.3k
0
gravatar for madk00k
7.1 years ago by
madk00k340
Heidelberg
madk00k340 wrote:

Most commonly used tools are

ADD COMMENTlink written 7.1 years ago by madk00k340
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