I have downloaded miRNA seq data for colon adenocarcinoma. As i am a beginner, i am facing difficulties to understand and interpret the data. I have miRNA seq files for all samples but how to find the file for the matched normal tissue? And how to study the expression of a particular miRNA across the whole sample set?
When you download data from TCGA, it includes a text file, named "FILE_SAMPLE_MAP". In this file you can find the patient codes as well as corresponding file names.
If you seek matched normal/tumor samples, you must note to the barcode of patients. The 'participant' part of barcodes must be the same. For more information about TCGA barcodes, please see this.