I am analyzing the transcriptome of arabidopsis and everything worked well till the cuffmerge. After running the cuffmerge i didnt get the merged gtf file.
Was there an error? What command did you use to run cuffmerge?
there is no error.
/home/naveen/Desktop/cufflinks-2.2.1.Linux_x86_64/cuffmerge -g /home/naveen/Desktop/Tamips_transcriptome_analysis/AtRTD2_19April2016.gtf -s /home/naveen/Desktop/Tamips_transcriptome_analysis/genomeindex/Genome -p 50 /home/naveen/Desktop/Tamips_transcriptome_analysis/cuffdiff_out/assemblies.txt
Did you solve the problem? I have same issue :'(