Hello all,
I'm working on a project where we will have transcriptome sequences to about 35x for ~45 individuals from a single population, grown up in 7 different treatments. We are interested in assembling a reference transcriptome and then assessing patterns of differential expression among all of the individuals by aligning to this reference.
We are planning to use Trinity to assemble the transcriptomes, but we were uncertain whether it would be best to try to 'merge' them together afterwards (using Minimus or CAP3 or similar) or to simply paste together the .fasta files into one large file before running them through Trinity and then sort it out afterwards. The individuals are not clones (lodgepole pine), so there will be allele variants to contend with in addition to splicing and errors.
Any thoughts?
Thanks!
I'm working on a project where we will have transcriptome sequences to about 35x for ~45 individuals from a single population, grown up in 7 different treatments. We are interested in assembling a reference transcriptome and then assessing patterns of differential expression among all of the individuals by aligning to this reference.
We are planning to use Trinity to assemble the transcriptomes, but we were uncertain whether it would be best to try to 'merge' them together afterwards (using Minimus or CAP3 or similar) or to simply paste together the .fasta files into one large file before running them through Trinity and then sort it out afterwards. The individuals are not clones (lodgepole pine), so there will be allele variants to contend with in addition to splicing and errors.
Any thoughts?
Thanks!
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