Removing genes found on two (or more) chromosomes from gtf file

Question

[arta]

Hi,

I am analyzing the rna-seq data in terms of significantly exon usage from DEXSeq. However, i have faced an error during preparation of annotation file for the main analyze. Here is the error;

raise ValueError, "Same name found on two chromosomes: %s, %s" % ( str(l[i]), str(l[i+1]) )

I realized some genes are annotated in multiple chromosomes in gtf file (grch38 hg38) and I need to remove them.

Any ideas & help ??

Thanks...

[Sej Modha]

It seems like something to do with the exon coordinates - https://support.bioconductor.org/p/44963/

[arta]

Well i know this might be another issue, but my first concern is removing that genes which are found on more than one chromosomes.

[Kevin Blighe]

From where did you download the GTF?; did you execute the dexseq_prepare_annotation.py Python script that comes with DEXSeq?