Question: Finding the Length Distribution of Structural Variations
0
gravatar for Amirosein
3.6 years ago by
Amirosein70
UBC, Vancouver, CA.
Amirosein70 wrote:

Hi

I am working on a simple algorithm to enable an aligner to handle structural variations, for the first step i need to know the distribution of the length of Structural Variations, for this purpose i need a database (or a reliable file)* providing structural variation information for me to calculate the distribution, anyone knows a database providing this for me? or any other way to this task?

the best thing i want is the estimated distribution but even knowing some statistics could be good, for example "90% of SVs are less than 200 bases long" or some other evident information like this.

the human genome SVs length Distribution will be good but having some wider information is better. *: update thanks everyone

structural variation sv • 1.0k views
ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by Amirosein70

for this purpose i need a database providing structural variation information for me to calculate the distribution, anyone

why do you need a database ? a simple text file and R would be enough , isn't it ?

ADD REPLYlink written 3.6 years ago by Pierre Lindenbaum124k

You just need the regions and calculate the length and plot the histogram in R for the column having the length, that is it.

ADD REPLYlink written 3.6 years ago by ivivek_ngs4.8k

yeah i need the regions, so where to get them?

ADD REPLYlink written 3.6 years ago by Amirosein70

yeah that could be good, but where?

ADD REPLYlink written 3.6 years ago by Amirosein70

"where" what ?

ADD REPLYlink written 3.6 years ago by Pierre Lindenbaum124k

i need a simple text file and then do this in R :) i need that information then i know what to do with it :) now the problem is the data itself, ""where to find the length of Structural Variation?"" thanks

ADD REPLYlink written 3.6 years ago by Amirosein70

i need a simple text file and then do this in R :) i need that information then i know what to do with it :) now the problem is the data itself, where to find the length of Structural Variation? thanks

ADD REPLYlink written 3.6 years ago by Amirosein70
0
gravatar for Amirosein
3.6 years ago by
Amirosein70
UBC, Vancouver, CA.
Amirosein70 wrote:

Poly Peak Parser will do it

published 2014 with this title:

Poly peak parser: Method and software for identification of unknown indels using sanger sequencing of polymerase chain reaction products.

it can find positions that deletions occurred in one of two sequenced strings

ADD COMMENTlink written 3.6 years ago by Amirosein70

common! kidding me? polypeakparser is a software to find heterozygous indels in sanger reads but not for structural variation detection.

ADD REPLYlink written 3.3 years ago by Amirosein70
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