I am working with STAR and I wonder whether it is posible to keep those reads that DO NOT map with the reference genome. I know that's can be done with other programs as Bowtie and hisat but I would like to do it with STAR since the positive alignment (those that do match) has been done with STAR.
In case it is not possible... do you think it would be a problem to run each of these alignment (positive and negative) with different programs? My aim is to merge these two .bam files and work with them as one. Would I have any problem with compatibility?
Thank you so much in advance.