Question: regarding Break dancer ouput
0
gravatar for DL
19 months ago by
DL20
India
DL20 wrote:

Hello,

Can anyone tell me description of breakdancer ouput :

Software: unstable (commit nogit)

Command: /usr/local/bioinfo/src/BreakDancer/breakdancer-1.3.6/bin/breakdancer-max -t -q 10 rose.cfg 

Library Statistics:

DI_sort.bam mean:976.56 std:415.44  uppercutoff:3204.9  lowercutoff:137.21  readlen:145.57  library:6   reflen:518514126    seqcov:52.2741  phycov:175.341  32:53392110

DK_sort.bam mean:1021.13    std:300.81  uppercutoff:2543.75 lowercutoff:214.78  readlen:145.58  library:7   reflen:518514126    seqcov:0    phycov:0


Chr1    Pos1    Orientation1    Chr2    Pos2    Orientation2    Type    Size    Score   num_Reads   num_Reads_lib   DI_sort.bam DK_sort.bam

Chr01   61421771    510+53- Chr00   403216  442+182-    CTX -976    99  286 DI_sort.bam|286

Chr01   47979608    354+513-    Chr00   953918  1005+884-   CTX -976    99  336 DI_sort.bam|336

Chr01   47979608    354+513-    Chr00   955163  462+465-    CTX -976    99  92  DI_sort.bam|92

Chr01   25443826    315+292-    Chr00   1380696 384+261-    CTX -976    35  157 DI_sort.bam|157

Chr01   59085904    554+453-    Chr00   1564801 186+372-    CTX -976    56  329 DI_sort.bam|329

Chr01   17496243    521+62- Chr00   2019749 215+375-    CTX -976    43  162 DI_sort.bam|162

Chr01   18611670    106+282-    Chr00   4915819 694+713-    CTX -976    99  261 DI_sort.bam|261

Chr01   7035116 263+202-    Chr00   5801157 985+428-    CTX -976    46  153 DI_sort.bam|153
sequencing next-gen genome • 559 views
ADD COMMENTlink modified 19 months ago by Samarth Kulshrestha170 • written 19 months ago by DL20
1
gravatar for Samarth Kulshrestha
19 months ago by
India
Samarth Kulshrestha170 wrote:

Deepika,

Breakdancer Output is well explained here (check the link):

https://github.com/kenchen/breakdancer

Hope this helps

ADD COMMENTlink written 19 months ago by Samarth Kulshrestha170

Hello Samarth,

Thank you for your reply. I have doubt in output of break dancer thats why i am asking this question. If you see 11 column that include DI_sort.bam|286 and so on... In my output file only DI library is supporting for CTX not the other library DK. So i have doubt that is there any mistake made by me during running breakdancer. It can be possible due to read group problem in libaray.

Thanks

ADD REPLYlink written 19 months ago by DL20

What i can see here, In the Library statistics section of DK_sort.bam:

DK_sort.bam mean:1021.13 std:300.81 uppercutoff:2543.75 lowercutoff:214.78 readlen:145.58 library:7 reflen:518514126
seqcov:0 phycov:0

Both coverage parameter, seq coverage (seqcov) and physical coverage (phycov) is 0 for DK_sort.bam on the other hand sequence coverage is 52 and physical coverage is 175 for DI_sort.bam . So, I suggest you to look into the DK_sort.bam carefully. This might be one of the reason breakdancer is not able to detect supportive read-pair of DK library.

Best

ADD REPLYlink modified 19 months ago • written 19 months ago by Samarth Kulshrestha170

Yes, i got the problem and solved it and thank you for help.

ADD REPLYlink written 19 months ago by DL20
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