I'm reading an article about enhancer RNA, and the author described it like this in the method section：
To identify and characterize the transcript features of eRNAs and uaRNAs, we performed de novo assembly of nascent transcriptome by the Stringtie algorithm (Pertea et al., 2015) on TT-Seq data, and we merged TT-Seq from two sets of biological replicates (TableS1). Both EtOH and E2 TT-Seq reads were merged as the input, and the Stringite was run with the parameter of -f 0.1,-c 2, -g 200,–rf and without reference guide. The de novo assembled transcriptome annotation files were first filtered by removing those overlapping any tRNA, snoRNA, miRNA, pseudo-gene and protein-coding genes annotated in GENCODE v19 (in the same strand).
I don't quite understand. What does the without reference guide mean by the author here? How can this be achieved?
Authors used stringtie in de novo mode. Read https://rnabio.org/module-05-isoforms/0005/02/01/Reference_Guided_Transcript_Assembly/ and https://rnabio.org/module-05-isoforms/0005/03/01/De_Novo_Transcript/