Would greatly appreciate if someone can explain to me the difference between the two BAM summary numbers, namely; "raw total sequences" and "sequences" that appears on the output of the Stats module in SAMTools.
I used Stats of SAMTools to generate summary statistics for a pooled BAM file. In the output I got, "raw total sequences" = "sequences". Does it mean that all my raw sequences were usable sequences and none were filtered out?
Best Rgds, Hasitha.