Hi,

I apologize in advance as this question might be rather basic. I have an alignment BAM file and I'd like to find out where base x on read y maps to on the reference sequence. In the end I would like to have a list of reference sequence coordinates which correspond to the location where every base of read y maps to. For example:

aligned read: AAGT-> 1,2,6,7 (mapping position on reference genome)

I saw that the GenomicAlignments package has a function called "mapFromAlignments" which sort of does what I want but I am not certain I have the right input to use it. Plus the problem seems easy in principle so I was wondering if there is a more straight forward way to do it.

Thank you already!