Create a GTF file from mapped reads

Question

[JulianC]

Hi!

How can I create a GTF (or SAF) file starting from mapped reads? Thanks!!

[h.mon]

Please elaborate on what you want to do. Do you want to perform a full-fledged annotation of a novel genome? Or do you want to find novel transcripts on an already annotated genome? Are your our reads RNAseq, DNAseq, ChIPseq, ...?

[JulianC]

Sorry, my reads come from miRNA seq. I want to find novel transcripts on an already annotated genome

Answer 1

[grant.hovhannisyan]

If this is RNAseq data, use Stringtie.