Hi I have H3k27 chip-seq data for our cancer cell lines. I am using bowtie2 for alignment to human genome. My FASTQC looks very good. I used global end-to-end alignment option but my # unique alignments are around 55% in IP and %69 in Input samples. I reran Bowtie2 with local option with sensitive and very sensitive options but # of unique alignments drop to 44% from 55% and multimappers increased.
Is there any way to increase the # unique alignments by changing some parameters or it is fine to have 55% unique alignments in case of H3k27 mark.?