search

schneebergerlab / syri

Synteny and Rearrangement Identifier
https://schneebergerlab.github.io/syri/
MIT License
306 stars 36 forks source link

INV and INVDUP check questions #146

Closed Chenglin20170390 closed 2 years ago

Chenglin20170390 commented 2 years ago

Hi Manish Goel,

I have a question about the result checking of SVs from syri. I have checked the mega-base INV by comparing synteny (dotplot) of the sequence and 2m flanked sequences from both reference genome and query genome based on syri.out This is show a good result checking of INV from syri.

image

However, when I checked the result from 100k INVDP by same methods (2k flanked sequence) , the most results look like below. I wondering whether my methods have some problem for checking INVDP? I also want to check INS DEL TRANSLOCATION based on dotplot to confirm my SVs set, do you think this is working or do you have any suggestion? minimap2 version 2.17

 Thanks in advance!
image
mnshgl0110 commented 2 years ago

I am not sure I get the exact question, but I think you are trying to validate the annotations by syri.

In the second figure there seems to be a INVDP (as marked below) image If syri predicted this, then it is correct.