Re: [Breakdancer-help] something about cpp version

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

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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