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

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7.0 years ago

arta ▴ 670

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...

gtf awk bash dexseq python • 1.7k views

ADD COMMENT • link 7.0 years ago by arta ▴ 670

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

ADD REPLY • link 7.0 years ago by Sej Modha 5.3k

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

ADD REPLY • link 7.0 years ago by arta ▴ 670

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

ADD REPLY • link 7.0 years ago by Kevin Blighe 88k

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