I am trying to run dexseq_prepare_annotation.py, but keep receiving the same error:
File "dexseq_prepare_annotation.py", line 129
raise ValueError, "Same name found on two chromosomes: %s, %s" % ( str(l[i]), str(l[i+1]) )
My guess is the problem is inside the gtf file, which was downloaded from Ensembl (hg19).
Hopefully someone can help me figure this out! Many thanks in advance.