How to use stringtie without reference guide

How to use stringtie without reference guide

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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

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