I really do agree in the time I spent as a graduate student and postdoc I saw so many questionable data "massaging" tricks that aren't including with the paper

I really do agree in the time I spent as a graduate student and postdoc I saw so many questionable data "massaging" tricks that aren't including with the paper methods. Oh the copy number segment doesn't cover the gene I'm interested in but it looks like it should be copy number 4 and not copy number 2, therefore; I will hand edit the file and fix these issues for all 100+ samples in my study. I think parts of this kind of "massaging" is slowly changing as more and more people push for open access data and open access code. Science would benefit greatly from having access to the raw data and code used to generate the conclusions of a given paper. As a graduate student there is some level of protection from a supervisor punishing you if you have differences in opinion but as a post-doc those kinds of protections are tossed out the window. I have a friend who was 3 years into their post-doc and had an argument with their principle investigator about the interpretation of their results and how their work would be published only to have their contract cancelled the next day. In the end keeping quiet probably would have got them at least a first author paper but they ended up with 3rd authorship on their own project.