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dieterich-lab / DCC

DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies a series of filters and integrates data across replicate sets to arrive at a precise list of circRNA candidates.
https://dieterichlab.org/software/
GNU General Public License v3.0
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Error in DCC running : missing file even after providing the file . #89

Closed manzaaa closed 3 years ago

manzaaa commented 3 years ago

Hello, It is a very good tool for circRNA detection. I am trying to use this tool and I'm running into an error. It would be great if you could help me with it. I mapped my reads to the reference genome using STAR and got the chimeric.out.junction and used it as the input for DCC. I used the following command

DCC --detect @female_heartChimeric.out.junction -R repeatmasker_human.gtf -an hg38.ensGene.gtf -B female_heartAligned_sorted.bam -F -M -Nr 5 6 -fg -G -A hg38.fa

This is the error I keep getting:

ERROR: Required file chr2 88111677 - chr12 122328366 + -1 0 0 D93Z3NS1:226:C75WFACXX:2:1101:2637:45497 88111678 101M 122328367 60M4560N41M is missing, exiting

Is it because of the repeat file or the annotation file ? I am not able to figure it out.

Thanks for your time Maanasa

tjakobi commented 3 years ago

Dear @manzaaa,

when providing the @female_heartChimeric.out.junction option, DCC treat every line of the file female_heartChimeric.out.junction as a file name and try to topen that file.

The correct call would be something like

DCC --detect female_heartChimeric.out.junction -R repeatmasker_human.gtf -an hg38.ensGene.gtf -B female_heartAligned_sorted.bam -F -M -Nr 5 6 -fg -G -A hg38.fa

Cheers, Tobias

manzaaa commented 3 years ago

Dear Tobias,

Thank you so much for the explanation. Was able to get it running!

Cheers, Maanasa