I ran Kallisto and Dsse2 to get my list of DE genes. In the results of Dseq2, I can see there are about 20000 lines - I am assuming 1 line for each gene. However, when I download the file, I only get 9000 lines. Can you please let me know why this is happening? And how can I download the entire dataset of 20000 lines?
Try the create/download “History Archive” method.
More details are in this prior Q&A:
Thank you! It worked