This is a test version of Biostars. For the public version, visit https://www.biostars.org.
regarding Break dancer ouput

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
genome next-gen sequencing
• 2,461 views • link
updated by Samarth Kulshrestha Samarth Kulshrestha • written by DL • DL

1 answer

Deepika,

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

https://github.com/kenchen/breakdancer

Hope this helps

• 0 views • link
written by Samarth Kulshrestha Samarth Kulshrestha

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

• 0 views • link
written by DL • DL

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

• 0 views • link
written by Samarth Kulshrestha Samarth Kulshrestha

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

• 0 views • link
written by DL • DL

Log in to answer this question.

More posts like this