When is recommended to remove or keep Unpaired "Orphan" reads in downstream analysis?
In NGS, after alignment, SAM and BAM files contain reads (paired and unpaired). I wonder when is better to keep the unpaired (orphaned) reads for the downstream analysis and when should be kept?
e.g. in RNA-seq, exome-seq, variant calling, structural variantion, methylation, Chip-seq... whatever comes through your mind is highly appreciated.
If your answer is supported by a paper or experience would definitely be great.
Thanks in advance