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suda-huanglab / circlehunter

A pipeline for identifying complex ecDNA using ATAC-Seq data.
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question about CUTSITE #11

Closed DaiyuanLiu closed 3 months ago

DaiyuanLiu commented 4 months ago

Dear Dr.Yang, Thanks for your useful tool. I have a question about the cutsites.py script that why the value of flag 83 is reference_start rather than reference_end? It seems that the "163: 'reference_start'" and "83: 'reference_start'" point to the same chromosome coordinate. Looking forward to your reply.

Snipaste_2024-03-07_15-53-22
yangmqglobe commented 4 months ago

I remember that cutsites.py is not used in the main pipeline, so it is not tested.

DaiyuanLiu commented 4 months ago

I remember that cutsites.py is not used in the main pipeline, so it is not tested.

But I found cutsites.py in accessible.smk, and found accessible.smk in "Snakefile". Can I take the "Snakefile" file as the main pipeline?

yangmqglobe commented 4 months ago

No, the main pipeline only include rules that generate result of rule all in Snakefile, please check out snakemake document

DaiyuanLiu commented 4 months ago

No, the main pipeline only include rules that generate result of rule all in Snakefile, please check out snakemake document

So the accessible.smk won't be run if I run Snakefile? The cutsites.py is invoked in the accessible.smk. image

yangmqglobe commented 4 months ago

Yes，the main pipeline use bam2bed.py to generete accessible tag.

DaiyuanLiu commented 4 months ago

Yes，the main pipeline use bam2bed.py to generete accessible tag.

The bam2bed.py is the first step of accessible.smk. What about the cutsites section? Is it useless? image

yangmqglobe commented 4 months ago

That may be a test steps, but I found that adjust Tn5 cutsize is not proper for ecDNA breakpoint calling, so that is not used.

DaiyuanLiu commented 3 months ago

That may be a test steps, but I found that adjust Tn5 cutsize is not proper for ecDNA breakpoint calling, so that is not used.

I got it. Thank you.