Hi everybody,
I'm working on RNA-seq analysis of non-model plant, my focus is on the root so the extracted RNA from roots of interest under various treatments has been sequenced on one lane of Illumina (totally 5 libraries). To generate the complete de novo transcriptome assembly, the total RNA extracted from roots, leaf and stem were also pooled (in equal amounts) and sequenced on another lane of Illumina. Therefore, I have two datasets, one from roots and another from roots, stem and leaf. I've made de novo assembly using sequencing reads of two datasets, separately. It sounds that both assemblies have good quality in base on some basic parameters. I'm not looking for an especial expressed gene(s) in roots; I would like to use the information of two datasets (two assemblies) for further analysis? Would you please let me know your suggestion and idea to this end?. Please consider I cannot do assembly using all sequencing reads of two datasets due to limited computational resources. Thanks in advance
