## RNA-seq / Map aligned reads to exons for DEXSeq

### Description

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.

### Parameters

- Does the alignment file contain paired-end data (yes, no) [no]
- Organism (human hg19.68, mouse mm10.68, mouse mm9.62, rat rn4.68) [human hg19.68]

### Details

Note that the chromosome names in your BAM file need to the chr prefix (e.g. chr1).

### Output

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".

### References

This tool is based on the HTSeq package by Simon Anders and it is available in the DEXSeq Bioconductor package.