RSeQC: Read Distribution is mostly UTR instead of exons for mRNA-seq

[jennaj]

@cscho

I am also having trouble later on in the workflow, where ‘Annotate DESeq2/DEXSeq output tables’ with the same GTF file as an input is resulting in an empty output. I’m wondering if the issues are related.

Hi @cscho

Thanks for including that extra info. The GTF format is certainly a good place to start checking.

General format tips are here: working-with-gff-gft-gtf2-gff3-reference-annotation

What pops out to me is the sort order of the GTF file in the last screenshot. The “transcript” features should be ordered before the “exon” features associated with them, not after.

For comparison, you could try one of the GTFs that UCSC provides. All three will work with the tools you mentioned. These are ready-to-use: copy/paste a file URL into the Upload tool using all defaults. Galaxy will uncompress, assign the correct datatype, and tools will recognize the dataset as valid GTF/GFF input. Index of /goldenPath/danRer11/bigZips/genes