lvree
commented
5 days ago Aah I'm sorry I see accidentally ran the call.cns file instead of the .cns file. But the output I got when using call.cns was the same as when I ran this part on my dataset: cnvkit.py batch Tumor.bam --normal Normal.bam \ --targets my_baits.bed --annotate refFlat.txt \ --fasta hg19.fasta --access data/access-5kb-mappable.hg19.bed \ --output-reference my_reference.cnn --output-dir results/ \ --diagram --scatter
Further it says this:
So why is the batch command then using call.cns instead of .cns as is stated?
I'm very new to CNV analysis and run across something I don't understand. As stated in the manual for the scatter command there are two options:
I assumed they would produce the same output, as it was only a shorthand.
But the first command produces this plot:
And the second produces this:
What does explain this difference in behaviour, or am I misunderstanding something? And can someone explain what the difference in the plots means? Like, why does one have sort of lines and the other has a lot of points? Also, why does the first have it lowest point around -2.5 and the second below -3? I didn't do any manual scaling of the y-axis here yet, so this is just standard output
Then also another thing when I zoomed in on one chromosome the lowest point visible is at -4:
But for the standard plot of the whole genome that isn't even in there, but when I lower the min size of the Y axis it is indeed in there:
Why does it cut the graph off when there are still points there? Is it because there are no orange points there?
Thank you very much!