I am analysing my ChIP-Seq data which generated by paired-end sequencing. But due to some experimental issues. It is better to mapping both the R1 and R2 data in single-end way separately.
So I would like to know how can I combine two SAM or BAM files into one file and how can I get the mapping statistics (eg. mapped and unmapped percentage, unique and multiple mapped percentage...) from the combined file.
Thanks a lot.