I am currently doing RNA-seq for 3 datasets (obtained publicly through NCBI-SRA), each dataset is for 1 individual and all three individuals have different conditions. (c9ALS, sALS, Control). I have successfully ran tophat, and cufflinks. I am now trying to use Cuffcompare/ cuffmerge to examine all the transcripts. However, I am having some difficulties. Cuffmerge would not run and sends out a message that says "Fatal error: Matched on Error
Error running cuffmerge. The output file is empty, there may be an error with your input file or settings.". And with cuffcompare, although it will run successfully and turn green, the files will be empty.
This is really strange to me, because my tophat and cufflink files are large and I am able to view splice junctions on IGB. (Though, through looking at splice junctions, I am under the impression that there should be multiple assembled transcripts but there is only 1, again this is looking at the files using IGB, maybe there is something wrong there as well?).
I am not very familiar with RNA-seq; very confused. Thank you very much in advance for all your help!
Thank you, Roxy Zhang