Did anyone fixed the problem? same problem happened here.
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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
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Originally posted by Gonza View PostHi 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
Thank you very much!
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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
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