#4 Error running CIRI with gff files

[Shrey Gandhi]

Hello

I am using CIRI 2.0.6 to identify circular RNAs in Frog for which I was using gff file to guide the annotaion. However it gives an error
"CIRI cannot understand GCF_001663975.1_Xenopus_laevis_v2_genomic.gff at CIRI2.pl line 459, <anno> line 1931950.</anno>"
(The gff file i use is from NCBI)

I went back to the gff file and checked this location. The problem seems to be because of the mitochondrial coordinates. Then I tried removing that particular line but got the same error. However, when I remove all the mitochondrial coordinates, it seems to work.

Can you tell me what is going wrong?
P.S. - The option -M NC_001573.1 doesn't seem to make any difference. Both with and without this, I get the same error.

[Yuan Gao]

Hi Shrey,

The reason seems to be no key word "gene=" found in exon features of mitochondrion in the gff file (for other chromosomes the key word exists). Removing all the mitochondrial features in the gff file will let CIRI do the right thing.

Thanks,
Yuan

[Shrey Gandhi]

Worked perfectly! Thanks :-)