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Old 12-03-2010, 11:53 AM   #1
Location: ny

Join Date: Jul 2009
Posts: 23
Default Bug? duplicated genes in cufflinks output genes.expr


When i supplied a reference gtf to cufflinks (-G), i found there are duplicated geneID in the output "genes.expr". That is a bit weird to me and it is very rare (3 out of 50k genes). I checked those 3 and it turns out that cufflink consider their isoforms as individual genes but still use the same gene_id supplied in the gtf file. All these 3 genes have a common characteristics. The genome positions of each isoform's transcript/exon/CDS are completely different. I guess cufflink use this information to judge whether different transcripts belongs to the same gene instead of using the gene_id information supplied in gtf.

I can remove them by hand but is there a way to "force" cufflinks to recognize them as a single gene?


original GTF file
chr06 SZ transcript 3851140 3853473 . + . gene_id "Os06g07923"; transcript_id "Os06g07923.2";
chr06 SZ CDS 3851140 3851247 . + 0 gene_id "Os06g07923"; transcript_id "Os06g07923.2";
chr06 SZ CDS 3853062 3853304 . + 0 gene_id "Os06g07923"; transcript_id "Os06g07923.2";
chr06 SZ exon 3853305 3853473 . + . gene_id "Os06g07923"; transcript_id "Os06g07923.2";
chr06 SZ transcript 3851392 3852964 . + . gene_id "Os06g07923"; transcript_id "Os06g07923.1";
chr06 SZ exon 3851392 3851900 . + . gene_id "Os06g07923"; transcript_id "Os06g07923.1";
chr06 SZ CDS 3851901 3852434 . + 0 gene_id "Os06g07923"; transcript_id "Os06g07923.1";
chr06 SZ exon 3852435 3852964 . + . gene_id "Os06g07923"; transcript_id "Os06g07923.1";

cufflinks output "genes.expr"
Os06g07923 141826 chr06 3851139 3853473 0 0 0 OK
Os06g07923 141826 chr06 3851391 3852964 0 0 0 OK
silin284 is offline   Reply With Quote
Old 12-13-2011, 08:12 AM   #2
Location: washington DC

Join Date: Oct 2011
Posts: 21

I have the same question. Why is cufflinks repeating genes?
apadr007 is offline   Reply With Quote
Old 02-24-2012, 02:48 AM   #3
Junior Member
Location: Heidelberg, Germany

Join Date: Nov 2009
Posts: 2

Dear silin

I think this is because in your reference annotation there are "unrelated" transcripts annotated to the same gene. I noticed that this happens, when there are independent transcript groups, i.e. groups of transcripts that do not overlap in exon coordinates. The can be side-by-side or one in the intron of the other. Some examples are in Ensembl 64


In some of these cases, I would say that Ensembl didn't follow its own guidelines, to assign the same gene identifier to transcripts with overlapping position, because there are clearly independent clusters.

I keep them and use the gene_id column of cufflinks to make tables unique.

kenphi is offline   Reply With Quote
Old 05-18-2014, 12:19 AM   #4
Location: Xi'an

Join Date: Apr 2013
Posts: 15

Another thread on this issue:

A solution based on mgogol's code:
emanlee is offline   Reply With Quote

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