[leejimmy93]

Did anyone fixed the problem? same problem happened here.

[Gonza]

Cufflinks duplicated genes error

Hi all,

I am not sure if this is a 'universal' answer, but the problem i was running into was in the gtf file. Cufflinks does not deal well with duplicated genes ID. In my particular case, i was using an old gtf file that must have had duplicates. Once i used the most updated one, i had no problem.

G

[leejimmy93]

Hi all,

I am not sure if this is a 'universal' answer, but the problem i was running into was in the gtf file. Cufflinks does not deal well with duplicated genes ID. In my particular case, i was using an old gtf file that must have had duplicates. Once i used the most updated one, i had no problem.

G

Hi, do you mean the duplicated gene ID in the reference gtf file or the gtf file generated by cufflinks? Also was your reference gtf file sorted? Can you please send me a screenshot of the gtf file that works and that doesn't work?

Thank you very much!

[Gonza]

Hi,

This is what i was getting.



[Fri Jan 6 12:35:41 2017] Beginning transcriptome assembly merge

-------------------------------------------

[Fri Jan 6 12:35:41 2017] Preparing output location ./merged_asm/

[Fri Jan 6 12:36:23 2017] Converting GTF files to SAM

[12:36:23] Loading reference annotation.

GFF Error: duplicate/invalid 'transcript' feature ID=Peaxi162Scf00002g00014.1

[FAILED]

Error: could not execute gtf_to_sam



Once i started to used an updated GTF/GFF file i had no problem. Not sure what species you're working with, but this problem will not occur if you are using one with well annotated features.

Good luck

[leejimmy93]

It turned out my problem was caused by the reference gtf/gff file too. Thank you very much!

[Gonza]

glad it worked!