Hi, I too have the same problem while using dexseq_prepare_annotation.py with UCSC annotation file. I am getting the following error: > Traceback (most recent call last): > File > "/work_space/software/external_downloaded_files/R-2.14.2/library/DEX Seq/python_scripts/dexseq_prepare_annotation.py", > line 91, in <module> > assert l[i].iv.end <= l[i+1].iv.start, str(l[i+1]) + " starts too > early" > AssertionError: <genomicfeature: exonic_part="" 'cfb'="" at="" chr6_dbb_hap3:=""> 3199308 -> 3199650 (strand '+')> starts too early Has anyone fixed this issue? Any help would be highly appreciated. -- Geetha Venkatesh Institute of Clinical Molecular Biology Christian Albrechts University Kiel Am Botanischen Garten 11 D-24118 Kiel, Germany g.venkatesh at ikmb.uni-kiel.de office: +49 - (0)431-5971879

Hi On 17/01/13 11:15, Geetha Venkatesh wrote: > I too have the same problem while using dexseq_prepare_annotation.py > with UCSC annotation file. I am getting the following error: >> Traceback (most recent call last): >> File >> "/work_space/software/external_downloaded_files/R-2.14.2/library/DE XSeq/python_scripts/dexseq_prepare_annotation.py", >> line 91, in <module> >> assert l[i].iv.end <= l[i+1].iv.start, str(l[i+1]) + " starts too >> early" >> AssertionError: <genomicfeature: exonic_part="" 'cfb'="" at="" chr6_dbb_hap3:="">> 3199308 -> 3199650 (strand '+')> starts too early > > Has anyone fixed this issue? Any help would be highly appreciated. These UCSC annotation files seem to create a lot of trouble. (Admittedly, this might also be cause we -- as loyal EMBL employees ;-) -- use Ensembl rather than UCSC for most things and hence test our software mainly with Ensembl data.) Could you grep the lines concerning gene 'CFB' and post them? Maybe we can see something. Maybe you could also remove all the lines regarding chromosome variants. If you leave only lines for "chr6" and remove everything with "chr6_...", this might solve the issue. (In fact, maybe try removing all lines form the GTF files that contain an underscore anywhere in the first field.) Unless you are doing something special, I guess you do not them anyway. Simon