I have done an alignment and used the -H option to dump the multiple hits as well as the -u option to dump the reads that do not map. However, after the alignment, I was interested in getting the numbers of hits in each category (# unique mapping reads, # reads that map to multiple places, and # reads that do not map). I converted the 'map' file to a 'txt' file and counted the number of lines (I got 8,335,894) and then I counted the lines in the non-mapping file (I got 4,575,039). However, this totals to the total number of reads that I started with (12,910,933)! What goes in the multi mapping file? I unzipped it, but cannot discern the format at all. Do the reads that map to multiple positions also go on the 'map' file?
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