Empty annotated transcript file

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1

Hi, can I kindly ask why the output generated by GFFCompare is empty (hence I could not use it to perform the downstream FeatureCounts analysis)

2

Hi @alina_chen,

Maybe try this tutorial: Hands-on: De novo transcriptome reconstruction with RNA-Seq / De novo transcriptome reconstruction with RNA-Seq / Transcriptomics

Compare the input files used for GFFcompare. Do they use the same chromosome/contig names? Note that many tools will treat chr1, Chr1 and 1 as different names.

What organism do you work with? Can you use any available annotation?

Kind regards,

Igor