Dear all,
i currently need to compare two transcriptomes - lets say, one untreated the other treated. Each of both cDNA-samples has been 36bp-paired-end-sequenced on two lanes (Illumina), such that i have 10e6 untreated and about 15e6 treated paired reads.
Primarily i want to discover structural changes in the treated transcriptome with respect to the untreated one. This includes genetic recombinations, splice variants and large transcriptional inserts similar to transposons.
My question is, how i could establish such an analysis. The recombination/inserts things make non-de-novo (hence comparative) assemblers appear inappropriate. Now, my initial idea is, to use Velvet/Abyss to build the two assemblies de novo, to align them in a second step against each other. Does this make sense to you guys? Or is there even a package out there, which i don't know yet?
Thanks in advance for any comments on that!
Cheers!
Winfried
i currently need to compare two transcriptomes - lets say, one untreated the other treated. Each of both cDNA-samples has been 36bp-paired-end-sequenced on two lanes (Illumina), such that i have 10e6 untreated and about 15e6 treated paired reads.
Primarily i want to discover structural changes in the treated transcriptome with respect to the untreated one. This includes genetic recombinations, splice variants and large transcriptional inserts similar to transposons.
My question is, how i could establish such an analysis. The recombination/inserts things make non-de-novo (hence comparative) assemblers appear inappropriate. Now, my initial idea is, to use Velvet/Abyss to build the two assemblies de novo, to align them in a second step against each other. Does this make sense to you guys? Or is there even a package out there, which i don't know yet?
Thanks in advance for any comments on that!
Cheers!
Winfried
