  I am trying to do exactly the same pipeline for RNA-seq data process as the TCGA does. Usually when we ask a sequencing service, we can get a fastQ file. It contains sequence and read quality information. The alignment step comes next.
  However in the case of TCGA, as their pipeline suggested ([https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/][1]). It seems that they used BAM files as one of the inputs. I was wondering why they used BAM files as inputs and how can I repeat what they did?
  In addition, why isn't there seem to be a adaptor trimming process?


  [1]: ![TCGA mRNA-seq pipeline schematic][1]https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/


  [1]: https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/images/gene-expression-quantification-pipeline-v3.png
https://gdc.cancer.gov/about-gdc/gdc-faqs - Read the answer to "How can I access GDC sequencing data in FASTQ format?"

Level 1 (aka the raw fastq) data is restricted; to request access to it, see instructions here: https://gdc.cancer.gov/access-data/obtaining-access-controlled-data

Adaptor trimming is unnecessary in RNA-seq read mapping; many papers have been written about it (e.g. https://academic.oup.com/nargab/article/2/3/lqaa068/5901066 ).