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Hi,
I posted the msg in wrong place,, so I quote it here. Sorry for the inconvenience...
I posted the msg in wrong place,, so I quote it here. Sorry for the inconvenience...
Originally posted by Qingl
Hi,
I am doing a project to prove that a new technique used would not cause structure variant in chromosome. I simulated 2 control datasets from the intact ref human chr1, and 2 experimental datasets from the human chr1 having a 500kb inversion. After bwa alignment and SVDetect analysis, links2compare doesn't find any common links hits between 2 control datasets or 2 experimental datasets
. But all of the datasets have hits in links2SV...For the control datasets, I can assume the hits are from random alignment error, so we can think of it as false positives or noise. But for the experimental datasets, I really expect the common links hits can be found as true structure variant... I checked the individual .sv.txt file, and found the 500kb invertion is only found in one experimental dataset,,, Would this mean the coverage depth is not enough? The coverage depth I used is 16x, and fragment size is 300bp with read length 100bp.
Would it be possible for any expert to give me some suggestions, if I want to use SV_detect to achieve the project goal? Or Any other suggestions?
Thank you in advance!
I am doing a project to prove that a new technique used would not cause structure variant in chromosome. I simulated 2 control datasets from the intact ref human chr1, and 2 experimental datasets from the human chr1 having a 500kb inversion. After bwa alignment and SVDetect analysis, links2compare doesn't find any common links hits between 2 control datasets or 2 experimental datasets
. But all of the datasets have hits in links2SV...For the control datasets, I can assume the hits are from random alignment error, so we can think of it as false positives or noise. But for the experimental datasets, I really expect the common links hits can be found as true structure variant... I checked the individual .sv.txt file, and found the 500kb invertion is only found in one experimental dataset,,, Would this mean the coverage depth is not enough? The coverage depth I used is 16x, and fragment size is 300bp with read length 100bp. Would it be possible for any expert to give me some suggestions, if I want to use SV_detect to achieve the project goal? Or Any other suggestions?
Thank you in advance!