ecDNA only from Chr10 and Chr11

[lanliting]

Hi:
I am using Circle-Map to detect ecDNA from circle-seq data(paired-end).
However, strangely, the output bedfiles show that ecDNAs only exist in Chr10 and Chr11, and another sample only in Chr10,11,12,13,14,15. I don't know if it is the truth or is caused by some errors. My input BAM files contains all the chromosome. And I check the log files, it shows some warnings:

Can these warnings contribute to the results above?

[iprada]

Hi,

Based on the time it took to finish, you had very little sequencing depth. Can you elaborate more on your data? Sequencing depth, circle enrichement procedure etc.

best,

Inigo

[lanliting]

Thank you，Inigo
Our circle enrichment was based on column chromatography followed by digestion of remaining linear chromosomal DNA with exonuclease. Then we use rolling circle amplification and shear the amplified DNA to an average target peak size of 300 bp for library preparation and sequencing(150bp, paired). We have sequenced 11G bases for each sample.

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[lanliting]

I still did not figure out this issue, could you give some instructions?

[iprada]

Dear Ianliting,

Your experimental set-up looks fine to me. However, the issue you are encountering doesn't seem related to Circle-Map per se. As it does not seem to be a software issue. In case you haven't done it already, I advice you to contact some experts on circular DNA purification that could help troubleshooting your project.

best,

Iñigo