I have downloaded RNA_Seq files for mRNAs in level 3 format from TCGA database. These files contain "read_counts".
Now, my supervisor emphasizes to do quality control steps, e.g. GC-content bias and length bias but I do not know anything about these procedures and how I can do them. My major is not biology and it is the first time I am working with RNA-Seq files.
I appreciate if anyone can help me and tell me how I can do such pre-processing steps.