Any programs for analyzing solexa transcriptome (alternative splicing) ?

[baohua100]

Any programs for analyzing solexa transcriptome (alternative splicing) ?

[Torst]

Any programs for analyzing solexa transcriptome (alternative splicing) ?

Do you have a reference transcriptome?
If so, does it contain alternatively spliced sequences?

[baohua100]

we have reference transcriptome 。 but one gene one transcript sequence

there are no alternative splicing information

[Melissa]

I wonder if Solexa reads, say 50bp can identify alternative splicing when you don't have a reference genome. How can we tell the alignment software to map the reads so we can find splice variant?

Alternative splicing has been reported using 454 reads. The longer reads is probably an advantage. Anyone has done similar work using Solexa reads?

[griffon42]

Tophat does a really nice job mapping splice junctions without a set of known splice sites. It works very well with short Solexa reads, though I presume it requires a certain degree of read depth.

[baohua100]

i have reads.fq (5 000 000 reads RNA-seq) genome.fa

when i use bowtie align the reads, it aligns 4 200 000 reads.

but when i use tophat align the reads, the output file accepted_hits.sam only contains 1 900 000 reads. junctions.bed file is blank.

[steven]

Any programs for analyzing solexa transcriptome (alternative splicing) ?

Gmorse from the french genoscope (PMID: 19087247). It works with short reads and does not require any reference transcriptome, as explained here. Maybe limited for very complex and dense transcriptomes though (human/mouse/etc).
With a reference transcriptome, if you want to assign a quantity to each splicing variant I only know about this flux capacitor. Maybe not fully stable yet. I'm sure a lot of similar projects are in progress.
(Disclaimer: I personally know these people, they are friends of mine -but don't worry, contrary to me they still work in academic research).

Much more is expected to come from the RGASP project. I'd suggest to keep an eye on this.
Then, there are commercial products that claim to address "alternative splicing", but I am curious about what they really do...
yours,
s.