[BioC] DEXSeq: problem with dexseq_prepare_annotation.py

[Geetha Venkatesh]

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/DEXSeq/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