Hi there! I have no bioinformatics background. Just started learning RNA sequencing from tutorials. So prior apologies for asking any basic questions. Today I have 2: A) How do I produce coverage plots like the ones in the attached figures? I have tried IGV but is there any way to do it via UCSC Genome Browser? I need the sense and antisense strand coverage in the same plot preferably.
B) Coverage plots are created from .BAM files. If I am comparing a WT and a Mutant sample by read coverage plots, how does it make sense if the exact same number of reads didn't end up in both samples? Increased number of Reads in the Mutant will automatically lead to greater read coverage of any particular feature right? Then how does it make sense to show read coverage without having proper controls? Many publications have such plots so obviously I am missing something. Or not understanding something basic?