Finding differentially expressed lncRNA
I’m trying to diff. expressed lncRNAs between two groups (of humans). I wanted to use the following pipeline: trimmomatic –> stringtie/cufflinks –> Cuffmerge/stringtie merge –> FEELnc to find lncRNAs.
To find diff. expressed transcripts I want to use the following pipeline: trimmomatic –> stringtie/cufflinks –> Cuffmerge/stringtie merge –> Cuffdiff/ballgown. However, I am somewhat confused about the following:
- in what step are the lncRNA GTF files produced by FEELnc used?
- is it not possible to skip FEELnc and use the grch38 lncRNA files on the gencode page?: www.gencodegenes.org/human/. What is the benefit of using FEELnc over just annotating to the gencode lncRNA GTFs – is it just finding novel lncRNAs in my samples?
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