Cufflinks Ids Doesn'T Match Between Different Annotations

Question

[PoGibas]

I want to compare two lncRNA annotations:

D. Kelley et al., 2012 and Cabili et al., 2011

curl -s "http://genomebiology.com/content/supplementary/gb-2012-13-11-r107-s7.gtf" > lncRNA_Kelley.gtf
curl -s "http://genesdev.cshlp.org/content/suppl/2011/09/01/gad.17446611.DC1/DataSet1.zip" | gunzip -c > lncRNA_Cabili.gtf

I noticed that Cufflinks IDs and genomic coordinates differ between those annotations, for example:

grep TCONS_00000841 lncRNA_Cabili.gtf
chr1    Cufflinks    exon    13997965    13998211    .    +    .    gene_id XLOC_000056 transcript_id TCONS_00000841 ...  
chr1    Cufflinks    exon    14000736    14001403    .    +    .    gene_id XLOC_000056 transcript_id TCONS_00000841 ...

Coordinates: chr1 13997965 13998211 & chr1 14000736 14001403
Gene id: XLOC_000056
Transcript id: TCONS_00000841

grep TCONS_00000841 lncRNA_Kelley.gtf
chr1    Cufflinks    exon    119682920    119683416    .    +    .    gene_id XLOC_000422 transcript_id TCONS_00000841 
chr1    Cufflinks    exon    119684370    119684436    .    +    .    gene_id XLOC_000422 transcript_id TCONS_00000841 
chr1    Cufflinks    exon    119689576    119689692    .    +    .    gene_id XLOC_000422 transcript_id TCONS_00000841 
chr1    Cufflinks    exon    119693188    119693369    .    +    .    gene_id XLOC_000422 transcript_id TCONS_00000841 
chr1    Cufflinks    exon    119721267    119726975    .    +    .    gene_id XLOC_000422 transcript_id TCONS_00000841

Coordinates: chr1 119682920 119683416 & chr1 119684370 119684436 & etc.
Gene id: XLOC_000422
Transcript id: TCONS_00000841

Should it be like this or is there some kind of mistake?

Answer 1

[Devon Ryan]

There's no reason to expect the XLOC_ gene id and TCONS_ transcript IDs to be consistent between different runs of cufflinks, which produced those. Those are just sequentially numbered IDs without any other particular meaning.