What it does
This tool appends the output table of DESeq2/edgeR/limma/DEXSeq with gene symbols, biotypes, positions etc. The information you want to add is configurable. This information should present in the input GTF/GFF file as attributes of feature you choose. DEXSeq-Count tool is used to prepare the DEXSeq compatible annotation (flattened GTF file) from input GTF/GFF. In this process, the exons that appear multiple times, once for each transcript are collapsed to so called exon counting bins. Counting bins for parts of exons arise when an exonic region appears with different boundaries in different transcripts. The resulting flattened GTF file contains pseudo exon ids per gene instead of per transcript. This tool maps the DEXSeq couting bins back to the original exon ids. This mapping is only possible if the input GTF/GFF file contains transcript identifier attribute for the chosen features type.
Inputs