I am working with tophat2 and cufflinks in order to try to align RNA-seq reads against an assembled genome. The reads I am using are for uninfected and infected Drosophila melanogaster larvae. I executed tophat2 on both files of reads, and then downloaded the assembled annotated transcript for chromosome 2L from the modENCODE fly database. When I try to then do cufflinks using one of the read files and chr2L as the reference annotation, I receive the following error message:
Error running cufflinks. return code = 1 Command line: cufflinks -q --no-update-check -I 300000 -F 0.100000 -j 0.150000 -p 8 -G /galaxy-repl/main/files/008/639/dataset_8639899.dat -u /galaxy-repl/main/files/008/639/dataset_8639595.dat [10:49:46] Loading reference annotation. Error: duplicate GFF ID '176550' encountered!
Any idea what is causing this error, and how to fix it? I tried the same exact methods described above with a different file of RNA-seq reads and it worked perfectly...
Thank you in advance for any assistance.