Given mapped reads in a BAM file, this tool counts the reads that fall into each non-overlapping exonic part using the script dexseq-count.py.
Note that the chromosome names in your BAM file need to the chr prefix (e.g. chr1).
Output is a table with counts for each non-overlapping exonic part. In order to use the output in DEXSeq, you need to select all samples and run the tool "Utilities - Define NGS experiment".
This tool is based on the HTSeq package by Simon Anders and it is available in the DEXSeq Bioconductor package.