Hi everybody, I've tried to do some DEXseq analysis in R, but first I know that I have to run some python scripts, is here when I get stuck. I'm working with mouse, and I downloaded gtf files from here and also from here, but when I run:
python R/x86_64-pc-linux-gnu-library/3.3/DEXSeq/python_scripts/dexseq_prepare_annotation.py gencode.mouse.annotation.gtf annot.mouse.DEXSeq.gff
I get this error message: F
File "/R/x86_64-pc-linux-gnu-library/3.3/DEXSeq/python_scripts/dexseq_prepare_annotation.py", line 129 raise ValueError, "Same name found on two chromosomes: %s, %s" % ( str(l[i]), str(l[i+1]) ) ^ SyntaxError: invalid syntax
I know that people have the same problems sometimes, but I couldn't find a way to fix it, some suggestions? Thanks!