Re: [Breakdancer-help] something about cpp version

[Ken C. <kc...@wa...>]

You could try the program Breakway on SOLiD data.

http://breakway.sourceforge.com

-Ken

On 7/19/10 9:53 AM, Ken Chen wrote:
> Hi hechuan,
>
>     The support to SOLiD data have not been fully examined.  Please 
> treat it with caution.  Thanks.
>
> -Ken
>
> On 7/19/10 3:14 AM, hechuan yang wrote:
>> Hi Ken,
>>
>> There are some problem  comes up when I use the new version of 
>> breakdancer.
>> The output of BreakdancerMax.pl and it's cpp version are different 
>> especially for the solid data.Let me show you some example:
>> [yanghch@submit1 solid]$ awk '$9>=60' s127.solid.max.c |type.count.pl 
>> <http://type.count.pl> -t7
>> DEL 160
>> INV 15
>> ITX 4
>> [yanghch@submit1 solid]$ awk '$9>=60' s127.solid.max.c.cpp 
>> |type.count.pl <http://type.count.pl> -t7
>> CTX
>> 297812
>> DEL 161
>> INS
>> 279
>> INV 15
>> ITX 4
>> [yanghch@submit1 solid]$ awk '$7=="CTX"' s127.solid.max.c |head
>> chr1 75803842 37+23- chr2 3042777 4+5- CTX -4731 0 2 NA|2 0.02 
>> BreakDancerMax-1.0r112 |g../solid/s127.solid.bed|C1
>> chr1 4948321 247+255- chr2 6037495 31+18- CTX -4731 0 2 NA|2 0.00 
>> BreakDancerMax-1.0r112 |g../solid/s127.solid.bed|C1
>> chr1 14397963 27+33- chr2 6037495 31+16- CTX -4731 0 2 NA|2 0.02 
>> BreakDancerMax-1.0r112 |g../solid/s127.solid.bed|C1
>> chr1 57157392 133+112- chr2 5016007 142+134- CTX -4731 0 2 NA|2 0.01 
>> BreakDancerMax-1.0r112 |g../solid/s127.solid.bed|C1
>> chr1 111486422 66+43- chr2 5016007 140+134- CTX -4731 0 2 NA|2 0.01 
>> BreakDancerMax-1.0r112 |g../solid/s127.solid.bed|C1
>> [yanghch@submit1 solid]$ awk '$7=="CTX"' s127.solid.max.c.cpp |head
>> chr1 75803842 37+23- chr2 3042777 4+5- CTX -4731 99 2 NA|2 0.0206186
>> chr1 4948321 247+255- chr2 6037495 31+18- CTX -4731 99 2 NA|2 0.00299401
>> chr1 14397963 27+33- chr2 6037495 31+16- CTX -4731 99 2 NA|2 0.0210526
>> chr1 57157392 133+112- chr2 5016007 142+134- CTX -4731 99 2 NA|2 
>> 0.00566572
>> chr1 111486422 66+43- chr2 5016007 140+134- CTX -4731 99 2 NA|2 0.0120482
>>
>> As you can see,the score for the same sv are not the same in the 
>> output of perl and cpp version of BreakdcerMax.And it's not only for 
>> the CTX data.
>>
>> Is the perl version more reliable?
>>
>> By the way,the bed format output file of cpp version have a flaw:
>>
>> track name=chr10_7096079_INS_-64        description="BreakDancer 
>> chr10 7096079 INS -64" useScore=0
>> chrchr10        7096068 7096142 5_mnOjLYels11|B 370     -       
>> 7096068 7096142 0,0,255
>> chrchr10        7096009 7096083 5_mnOjLYels11|B 370     +       
>> 7096009 7096083 255,0,0
>> chrchr10        7096074 7096148 7_Lr9qMMiJ321|B 370     -       
>> 7096074 7096148 0,0,255
>> chrchr10        7096057 7096131 7_Lr9qMMiJ321|B 370     +       
>> 7096057 7096131 255,0,0
>>
>> Best wishes.
>>
>> -- 
>> Hechuan Yang
>> Kunming Institute of Zoology,CAS
>> Kunming,Yunnan
>> P.R.China
>>
>>
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