Cuffcompare and cuffmerge using the genocode annotation file

[per_ngs]

Hi All,
I am trying to perform the cuffmerge operation on a couple of samples after cufflnks. I am using the gencode.v12.annotation.gtf as the reference file. My command is as follows
cuffmerge -o CN_cuffmerge -g gencode.v12.annotation.gtf Assembly_GTF_list.txt

Cuffmerge fails with the following error
[Sun Oct 28 23:39:46 2012] Comparing against reference file gencode.v12.annotation.gtf
Warning: Could not connect to update server to verify current version. Please check at the Cufflinks website (http://cufflinks.cbcb.umd.edu).
Error: duplicate GFF ID 'ENST00000361547.2' encountered!
[FAILED]
Error: could not execute cuffcompare

Curiously, when i run cuffcompare separately using the same gtf file and it works (from another thread on seqanswers it appears that this might be because of cuffmerge does a RABT).

Same issue was posted here http://seqanswers.com/forums/showthread.php?t=21364 by somebody else, but there were no replies to it. Hence trying one more time. Help greatly appreciated.

Regards,
ngs_newbie

[JQL]

What is gencode gtf? I have used ensembl or iGenome's gtf, but not aware of gencode. Can you explain? thanks

Hi All,
I am trying to perform the cuffmerge operation on a couple of samples after cufflnks. I am using the gencode.v12.annotation.gtf as the reference file. My command is as follows
cuffmerge -o CN_cuffmerge -g gencode.v12.annotation.gtf Assembly_GTF_list.txt

Cuffmerge fails with the following error
[Sun Oct 28 23:39:46 2012] Comparing against reference file gencode.v12.annotation.gtf
Warning: Could not connect to update server to verify current version. Please check at the Cufflinks website (http://cufflinks.cbcb.umd.edu).
Error: duplicate GFF ID 'ENST00000361547.2' encountered!
[FAILED]
Error: could not execute cuffcompare

Curiously, when i run cuffcompare separately using the same gtf file and it works (from another thread on seqanswers it appears that this might be because of cuffmerge does a RABT).

Same issue was posted here http://seqanswers.com/forums/showthread.php?t=21364 by somebody else, but there were no replies to it. Hence trying one more time. Help greatly appreciated.

Regards,
ngs_newbie

[dgaston]

Gencode is the gene definitions from the ENCODE project, so an alternative to Ensembl, UCSC, etc.

JQL: I am having the exact same problems. Doing some grepping on the file I don't see duplicate IDs, or at least it isn't apparent to me that they are actually duplicated. Similar errors people seem to have solved by either finding and deleting duplicate IDs from the annotation file.

Have you solved this yet? I am thinking on just switching to Ensembl but other people seem to be using GENCODE annotations just fine.