Hi all,
I was wondering what the best way to assemble a genome transcriptome(sorry, I typed down genome instead of transcriptome) from human RNA-seq data would be; I've looked at Trinity, AByss and the like, but I am a bit lost in the process of choosing between these software. It seems like these programs work far better with smaller genomes, so I was wondering if there were any more human oriented assembling programs. Additionally, I was wondering whether one would use multiple sets of RNAseq data to aid in assembling a transcriptome (the same sample/cell type has been sequenced multiple times) . I have not seen anything about this yet, but that may also be because I haven't looked hard enough.
Thanks for reading this!
Edit:
I should probably add that the reads are generally over 100 million in count and average around 50bp per read.