How can I create a GTF (or SAF) file starting from mapped reads? Thanks!!
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, ...?
Sorry, my reads come from miRNA seq. I want to find novel transcripts on an already annotated genome
If this is RNAseq data, use Stringtie.
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