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Question: Cufflinks duplicate GFF ID error
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gravatar for jingshuowang
3.9 years ago by
jingshuowang • 10
Germany
jingshuowang • 10 wrote:

I think this is an old but common problem that many people encountered when running the cufflinks with the ENsemble annotation references.

I have modified the annotation file download from Ensembl (GRCh37.V75). When I selected the option -G (use reference annotation), the cufflinks could successfully ran. However, when I selected the option -g (use reference annotation as guide), the cufflinks running was failed, showing the  duplicate GFF ID error. Does anybody have the same problems, or you may give me some suggestions.explanations on such problems.

I used the canonical genome reference GRCh37_Ensemble_75 (without unplaced contigs). 
rna-seq cufflinks • 1.4k views
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modified 3.9 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.9 years ago by jingshuowang • 10
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gravatar for Jennifer Hillman Jackson
3.9 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Duplicated GFF IDs are not accepted as input with this tool. As an alternative, consider the iGenomes version: 
http://support.illumina.com/sequencing/sequencing_software/igenome.html

Best, Jen, Galaxy team
ADD COMMENT • link written 3.9 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen,

Thanks for suggestion.

I definitely downloaded the reference annotation from iGenome (2014-05-23, the latest version), and made some modification to fit the genome reference (hg19 canonical):

1) change chromosome 1, 2, 3,.. to chr1, chr2, chr3,...

2) remove all of annotation information of unplaced contigs, just keep the annotation information of the "regular" chromosomes (chr1-22, chrX, chrY and chrM). And the order is chr1,chr10, chr11, ...chr19, chr2, chr20, chr21, chr22, chr3, ...chr9, chrM, chrX and chrY.

Is somthing wrong?

ADD REPLY • link written 3.9 years ago by sunnj85 • 0
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