how does annotate circular RNA ?
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11 months ago
modarzi ▴ 160

Hi,

Through running the CIRIquant package, I detect circular RNA info such as below:

Genome_Position              strand circ_type    gene_id      gene_name   gene_type

chr12:124904503|124934413   -          exon      ENSG00000196498.9     NCOR2    protein_coding

Now, I need to convert Genome_Position (chr12:124904503|124934413) to "circ name" such as "hsa_circ_0000519".

How and through which package or website can this convert? I appreciate it if anybody shares her/his comment with me.

Best,

R Genome circular RNA Position • 601 views
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11 months ago
Barry Digby ★ 1.0k

Most papers go something like this:

CircRNAs were annotated based on chromosomal location and the overlap with three circRNA databases: circAtlas v2 (16), circBase (17), and CIRCpedia v2 (18).

Download the database files and use bedtools intersect or variations thereof.

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Dear Barry, Thank you for your comment. practically, you mean I have to download 3 circRNA databases in .bed format. then merging them. am I understanding what you mean correctly?

I appreciate it if you explain more about your solution.

Best Regards,

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Yep - merging databases is a good strategy. You might have to format their outputs to conform to bed specifications (not too hard :) )

Convert the CIRIquant file into a basic BED file (tab delimited):

chr12    124904503    124934413    -

Then overlap it with the database bed file. CircBase provides hg19 circs in bed: http://www.circbase.org/download/hsa_hg19_circRNA.bed

bedtools intersect -a hsa_hg19_circRNA.bed -b biostars.txt -f 1.00
chr12   124911167   124922542   hsa_circ_0029311    1000    -   124911167   124922542   0,0,255 4   179,94,173,67   0,2991,3993,11308
chr12   124911167   124934413   hsa_circ_0000461    1000    -   124911167   124934413   0,0,255 5   179,94,173,67,53    0,2991,3993,11308,23193
chr12   124915160   124922542   hsa_circ_0029313    1000    -   124915160   124922542   0,0,255 2   173,67  0,7315
chr12   124922475   124934413   hsa_circ_0029314    1000    -   124922475   124934413   0,0,255 2   67,53   0,11885

Looks like there is no 100% overlap for your circRNA. It probably uses different exons in the NCOR gene. You can just name your circ as chr12:124904503|124934413

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