CIRCexplorer2: Exon count

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6.7 years ago

k.mamoud ▴ 10

Dear all

I am using CIRCexplorer2, to align and to find circRNA in mouse. I would like to do some differential expressiona analysis by using the exons that have been used to make my circRNA.

I would lkie to know which file I sould use to get the exons that have been used for each of my circRNA. And then where I can find the number of reads that are belonging to each of my exon, if it is possible?

Best regards

Mohamed

circRNA RNAseq count diffexp • 2.3k views

ADD COMMENT • link updated 5.6 years ago by nedoluzhko • 0 • written 6.7 years ago by k.mamoud ▴ 10

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Hi,

When you will run CIRCexplorer2 it will give you a file name "circularRNA_known.txt" which will contain all information related to circular RNA and the read counts.

Column number "10" will give you information related to "Exon_count" and column number "13" will give you info related to read count of that particular exon.

Hoping it will help you.

ADD REPLY • link 5.6 years ago by archana.bioinfo87 ▴ 210

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I have the same question. Any ideas?

ADD REPLY • link 5.6 years ago by nedoluzhko • 0

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