’-d‘ parameter mentioned in subsection 'Classification of assembly errors' of 'Methods section about craq HOT 6 CLOSED

from craq.

Wow! Many thanks for your detailed explanation, that helps me a lot.

I also have one more question that in your Supplementary file

Since the contig length is 10Mb and according to your description, the length of sliding window size is 0.0001* total assembly size, which should be 10Mb (10,000,000) * 0.0001 = 1000 b (1kb), not 10kb block region, and also, the 'L' of AQI calculation should be 1 based on mega-base unit to have 74 or 83 AQI value, but since the assembly size is 10Mb, which I think the 'L' should be 10 and I can't get the same value to AQI.

I am not sure to this part, Looking forward to your reply, thanks~ : )

from craq.

Sorry for the late reply, I've been traveling on business recently. The setting for our window is calculated based on the total size, not the length of a single contig. Additionally, I'm just using this chart to express our strategic thinking, 'To avoid excessive impacts of specific regions enriched in errors on the overall AQI values.' The 10M and 10kb in the picture have no actual significance.

from craq.

Here, you could assume the total size (L) is set to be 100M. And for one contig (e.g., contig1 = 1M, and there are 3 CREs located in a 10Kb window in contig1. The calculation for contig1’s AQI would be 100e^-0.1*(1+1/2+1/3)/1 = 83. The following scenario might be easier to understand and closer to reality.

from craq.

contig2

from craq.

I see, many thanks for your patience and clear explanation! Hope you doing well~

from craq.