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Hi Guys and Gals,
I am trying to analyze some RNA-seq data from a species without a Genome and all that jive. A assembled putative transcritptomes with Velvelt, Trans-Abyss, and Trinity and used CAP3 and CD hit to link assemble those to an EST collection. I used that CLC Genomics Workbench to map the sequences, but I do not want to depend on proprietary software for anything is this life (it is enough that I need to use MS Word). So is Bowtie still the best solution (as the manual says it will work with fragmented reference)? Can you use TopHat in the absence of a splice junction library and would that be worth it (given that as far as I understand, that would be basically bowtie)? Lastly, last say I have a very poorly assembled genome draft, is that better than the de-novo transcriptome?
Thank you!
Tiago
I am trying to analyze some RNA-seq data from a species without a Genome and all that jive. A assembled putative transcritptomes with Velvelt, Trans-Abyss, and Trinity and used CAP3 and CD hit to link assemble those to an EST collection. I used that CLC Genomics Workbench to map the sequences, but I do not want to depend on proprietary software for anything is this life (it is enough that I need to use MS Word). So is Bowtie still the best solution (as the manual says it will work with fragmented reference)? Can you use TopHat in the absence of a splice junction library and would that be worth it (given that as far as I understand, that would be basically bowtie)? Lastly, last say I have a very poorly assembled genome draft, is that better than the de-novo transcriptome?
Thank you!
Tiago