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Hi,
does everyone heard about assembly-free/reference-free expression analysis tools?
We have a species with no reference available and the idea is to study gene expression changes after some stimulus. First, we sequenced RNA of treated and non-treated samples and tried to make an assembly and to use it as reference. But all attempts of de novo assembly give poor results (about 100 thousands of short contigs). We tried a lot of differents programs and parameters; for other species that we are working with the results are much better so there is something in this species that hampers the assembly (most probably, high heterozygosity). I despaired of ever succeeding with the assembly and started to think whether there is other way to work with these data.
The changes in expression that we are looking for should be drastic and rather qualitative than quantitative. And the reads are pretty long (250+250 bp) - comparable to Sanger ESTs. Probably there are some approaches developed for ESTs that allow using such data without assembly?
does everyone heard about assembly-free/reference-free expression analysis tools?
We have a species with no reference available and the idea is to study gene expression changes after some stimulus. First, we sequenced RNA of treated and non-treated samples and tried to make an assembly and to use it as reference. But all attempts of de novo assembly give poor results (about 100 thousands of short contigs). We tried a lot of differents programs and parameters; for other species that we are working with the results are much better so there is something in this species that hampers the assembly (most probably, high heterozygosity). I despaired of ever succeeding with the assembly and started to think whether there is other way to work with these data.
The changes in expression that we are looking for should be drastic and rather qualitative than quantitative. And the reads are pretty long (250+250 bp) - comparable to Sanger ESTs. Probably there are some approaches developed for ESTs that allow using such data without assembly?
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