Entering edit mode
2.9 years ago
modarzi
▴
170
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,
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,
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):Then overlap it with the database bed file. CircBase provides hg19 circs in bed: http://www.circbase.org/download/hsa_hg19_circRNA.bed
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 aschr12:124904503|124934413