For Differential Gene Expression , which indexing format is better: GFF or GTF?

Question

[Fizzah]

Hello, I am working on DGE and wish to create reference index for mapping. Two file formats are used for it GFF and GTF. My question is:

What is the major difference between GTF and GFF? Which is better for DGE analysis? Which site provides GTF format for Gossypium hirsutum? Note: I have searched cottengen and phytozome and both gives GFF format?

[ATpoint]

You do not necessarily need a GTF. RNA-seq can be quantified directly against a transcriptome in fasta format using salmon. This will give you counts per transcript and currently (based on recent literature) seems to be more sensitive for DE analysis, and is much faster than traditional alignment and requires less memory. As one gene can have multiple transcripts, and as RNA-seq is commonly anaysed on gene-level you summarize the transcript level to the gene level with tximport and this can seamlessly go into the DE analysis software DESeq2.

See for a guided tutorial: https://bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html