How to use stringtie without reference guide
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6 months ago
LeeLee ▴ 20

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?

stringtie Bioinformatics • 304 views

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