I am making RNA-Seq libraries from mouse tissue for de-novo transcriptome assembly. I am planning to use cufflinks for this (the genome guided denovo assembly approach). What insert size is optimal for this? Since we are aligning to a well annotated genome, does it make sense to have a higher average insert size? This way, many more reads will span more than one exon with paired end sequencing, Won't this boost chances of finding alternative spliced isoforms? But does this entail sacrificing info on 3' and 5' end which is equally important (an important goal of our study is to find alternate 3' ends of genes)?
Thanks for your inputs!
Thanks for your inputs!
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