I have another question regarding mapping. These may be very simple ones but since I'm new to this kind of analysis I need assistance from people with experience.
According to many, mapping tools are now capable of handling poor quality bases. So I decided to map a data set with BWA MEM as it is without QC even though quality degrades towards 3' end. And also to perform some trimming at 3' end for the same data set and then do the mapping.
I'm going to use bedtools coverage,genomecov OR samtools stats to generate mapping statistics for the above 2 cases to see what mapping is better. Do you think this would give me a fair answer?
Thanks in advance.