Circle-Map Output File about circle-map

[iprada]

Dear Abdul,

-My question is, How can I apply filter on my output bed file to know the reads evidence of my circular DNA?

I am not sure if I understand your question. I will assume that you want to remove the circular DNA that do not have enough split reads. Let me know if I am wrong.

You can do this in many ways. For example, using gawk:

cat my_circles.bed | gawk '$5>4' > filtered_circles.bed

This command will remove all the circular DNA not containing at least 5 split reads.

Best regards,

Iñigo

[Abdubidopsis]

Yes, you are right. You got my question, thanks. I have one more question, Can I apply a one time filter on the same way from column #5 to column #11, to get the most cleaned and good quality circular DNA in a single file?

[iprada]

Dear Abdul,

Yes, of course.

cat my_circles.bed | gawk '$5>4' | gawk '$11<=0.2' > filtered_circles.bed

In this way you will get circles with at least 5 split reads, and, covered by sequencing at 80%.

Best wishes,

Iñigo

[Abdubidopsis]

Thanks.

[Abdubidopsis]

The question is related to the above discussion, I want to know how can i find the corresponding genes of these circular DNAs? please tell me, I will be glad to know about the genes of my circular DNA.

[iprada]

Dear Abdul,

That is outside the scope of Circle-Map. I encourage you to look at Bedtools software to do that.

I am closing the issue since it is not related to Circle-Map. Please, feel free to open a new issue if you have any questions regarding Circle-Map.

Best wishes,

Iñigo