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Old 06-27-2017, 06:11 PM   #1
Location: Wuhan, China

Join Date: Oct 2013
Posts: 20
Default How to extract the circRNA sequences based on the the back-spliced junctions detected

Dear All,

I have used several tools (findcirc, Circexplorer, DCC) to detect the circRNAs from mouse tissue. I have generated a list containing back-spliced junctions for each circRNA detected. An example for some circRNAs is given below

Chr Start End Strand
chr1 5089009 5098133 -
chr1 5093363 5133262 -
chr1 7120194 7120615 -
chr1 8414203 8448132 +
chr1 8554725 8595542 +
chr1 8554725 8607152 +
chr1 8583205 8595542 +
chr1 8583205 8607152 +
chr1 8624779 8682029 +

I'm wondering if there is a script or tool that can be used to extract the exon sequences of circRNAs detected. These circRNA sequences will be used for scanning miRNA binding sites.

The reference genome is mm10 and the gene annotation I used is gencode.vM14.annotation.gtf.

Any advice is very appreciated. Thank you very much!

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