I want to align my NGS data with human+ viral genome (concatenate form). It ideally output in following alignments
1- Reads only matched to human genome
2- Reads only matched to viral genome
3- Reads matched to both human plus viral genome
4- Reads one end mapped to either genome but other end unmapped
5- unmapped reads
My question is how to get all this information after alignment with Bowtie2 or BWA-MEM. After sensitive end-end alignment with Bowtie2, I only get BAM files and mapped or unmapped files. Here I have no idea how to find concatenate reads.
Is their any way to get all alignments as mentioned above (1-5). I want to know the viral integration sites.
Thanks in advance