Sorry for another inquiry, I am also wondering some advices on how to properly handles the differential analysis once I get the TElocal count. In my case, I am considering hundreds of cancer samples (hundreds of TElocal cntTable files), along with hundreds of normal samples cntable files. From my experience, DESeq2 will be very slow handling such large number of samples. Right now I just use raw count and calculate the log fold change between median values, but it's certainly a quick but ad-hoc solution, so try to reach out and inquire in case there are any recommendations.
Hello,
Sorry for another inquiry, I am also wondering some advices on how to properly handles the differential analysis once I get the TElocal count. In my case, I am considering hundreds of cancer samples (hundreds of TElocal cntTable files), along with hundreds of normal samples cntable files. From my experience, DESeq2 will be very slow handling such large number of samples. Right now I just use raw count and calculate the log fold change between median values, but it's certainly a quick but ad-hoc solution, so try to reach out and inquire in case there are any recommendations.
Thank you, Frank