The explosion of high throughput sequencing technologies marked a turn in our way of understanding the complexity and diversity of the transcriptome, including noncoding transcription dependent on RNA polymerase II. Many new ncRNA populations were described in recent years, including for example TSS RNAs, lincRNAs, eRNAs, PROMPTS and several others. Besides the advances in the average depth coverage of RNA-seq experiments, various additional protocols are now available that can be used to address qualitative and quantitative aspects of the noncoding transcriptome complexity and function. In this review, we will focus on methods allowing isolation and characterization of complex RNA populations using sequencing based approaches, including conventional strategies already used for coding genome and more specific developments allowing, for example, the study of nascent strand transcription, protein-bound or structured RNAs.