[Breakdancer-help] something about cpp version
Status: Beta
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From: hechuan y. <yan...@gm...> - 2010-07-19 08:14:53
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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 '$9>=60' s127.solid.max.c |type.count.pl -t7 DEL 160 INV 15 ITX 4 [yanghch@submit1 solid]$ awk '$9>=60' s127.solid.max.c.cpp |type.count.pl-t7 CTX 297812 DEL 161 INS 279 INV 15 ITX 4 [yanghch@submit1 solid]$ 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 |