Question: BreakDancer is giving blank output!
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4.8 years ago by
United States
anshuman.mit0 wrote:

I am not sure what I am doing wrong, but whenever I am running BreakDancer to detect translocation, I am getting a blank output. Please help me identify and fix the problem.


This is what the output of bam2cfg (filename : 'config_0040.cfg') looks like :

readgroup:Wk40_S08 platform:Illumnia map:Wk40.bam readlen:131.96 lib:S08 num:9997 lower:0.00 upper:590.70 mean:170.13 std:77.16 SWnormality:-63.17 exe:samtools view
readgroup:Wk40_S09 platform:Illumnia map:Wk40.bam readlen:140.85 lib:S09 num:9995 lower:0.00 upper:490.47 mean:174.70 std:62.52 SWnormality:-50.83 exe:samtools view
readgroup:Wk40_S07 platform:Illumnia map:Wk40.bam readlen:138.60 lib:S07 num:9992 lower:0.00 upper:584.92 mean:180.75 std:74.16 SWnormality:-60.15 exe:samtools view
readgroup:Wk40_S10 platform:Illumnia map:Wk40.bam readlen:131.90 lib:S10 num:9998 lower:0.00 upper:559.44 mean:164.77 std:72.51 SWnormality:-61.62 exe:samtools view
readgroup:Wk00_S04 platform:Illumnia map:Wk00.bam readlen:145.00 lib:S04 num:9993 lower:0.00 upper:595.78 mean:204.00 std:79.92 SWnormality:-57.13 exe:samtools view
readgroup:Wk00_S03 platform:Illumnia map:Wk00.bam readlen:133.13 lib:S03 num:9985 lower:0.00 upper:590.55 mean:168.25 std:73.59 SWnormality:-63.19 exe:samtools view
readgroup:Wk00_S02 platform:Illumnia map:Wk00.bam readlen:136.76 lib:S02 num:9985 lower:0.00 upper:527.69 mean:168.54 std:66.25 SWnormality:-60.85 exe:samtools view
readgroup:Wk00_S05 platform:Illumnia map:Wk00.bam readlen:137.73 lib:S05 num:9991 lower:0.00 upper:489.42 mean:166.33 std:60.46 SWnormality:-57.54 exe:samtools view


Then when I run the command below to find translocation events

perl -t config_0040.cfg > tres_0040.txt

This is what the entire output file 'tres_0040.txt' looks like (blank as in nothing below the header line "#Chr1 Pos1 Orientation1 ...") :


#Wk00.bam mean:166.330 std:60.460 uppercutoff:489.420 lowercutoff:0.000 readlen:137.730 library:S05 reflen:3051413885 seqcov:0.842x phycov:0.508x        
#Wk00.bam mean:204.000 std:79.920 uppercutoff:595.780 lowercutoff:0.000 readlen:145.000 library:S04 reflen:3051413885 seqcov:3.394x phycov:2.388x        
#Wk40.bam mean:174.700 std:62.520 uppercutoff:490.470 lowercutoff:0.000 readlen:140.850 library:S09 reflen:3051413885 seqcov:1.141x phycov:0.708x        
#Wk40.bam mean:180.750 std:74.160 uppercutoff:584.920 lowercutoff:0.000 readlen:138.600 library:S07 reflen:3051413885 seqcov:2.460x phycov:1.604x        
#Wk40.bam mean:170.130 std:77.160 uppercutoff:590.700 lowercutoff:0.000 readlen:131.960 library:S08 reflen:3051413885 seqcov:0.631x phycov:0.407x        
#Wk00.bam mean:168.540 std:66.250 uppercutoff:527.690 lowercutoff:0.000 readlen:136.760 library:S02 reflen:3051413885 seqcov:1.762x phycov:1.086x        
#Wk00.bam mean:168.250 std:73.590 uppercutoff:590.550 lowercutoff:0.000 readlen:133.130 library:S03 reflen:3051413885 seqcov:7.067x phycov:4.465x        
#Wk40.bam mean:164.770 std:72.510 uppercutoff:559.440 lowercutoff:0.000 readlen:131.900 library:S10 reflen:3051413885 seqcov:1.297x phycov:0.810x        
#Chr1 Pos1 Orientation1 Chr2 Pos2 Orientation2 Type Size Score num_Reads num_Reads_lib Allele_frequency Version Run_Param


I tried the same for 3 other bam file pairs, and the BreakDancer output file in all cases was blank, i.e. nothing below the header line "#Chr1 Pos1 Orientation1 ...". So how do I fix this problem?

In case it matters, I am running BreakDancer in the Terminal of my MacBook Pro (OS X Yosemite, Version 10.10.1).

rna-seq breakdancer • 1.3k views
ADD COMMENTlink modified 4.7 years ago by ernfrid380 • written 4.8 years ago by anshuman.mit0
gravatar for ernfrid
4.7 years ago by
Saint Louis
ernfrid380 wrote:

As far as I know the original BreakDancer perl script is unmaintained at this point. You may want to try using the latest version:

ADD COMMENTlink written 4.7 years ago by ernfrid380

Hi ernfri:

      When I used BreakDancer (1.4.5) for my bam file. Here's my command:

breakdancer/lib/breakdancer-max1.4.5/ -g -h MY.bam

      And I only got such result:

[Thu Jan 29 07:24:47 2015 breakdancer/lib/breakdancer-max1.4.5/] Processing bam: MY.W.HQ.ST_S.bam
[Thu Jan 29 07:24:50 2015 breakdancer/lib/breakdancer-max1.4.5/] selected_libs is : 1
[Thu Jan 29 07:24:50 2015 breakdancer/lib/breakdancer-max1.4.5/] Closing BAM file
[Thu Jan 29 07:24:50 2015 breakdancer/lib/breakdancer-max1.4.5/] Send TERM signal for 52630
[Thu Jan 29 07:24:52 2015 breakdancer/lib/breakdancer-max1.4.5/] samtools pid process 52630 is still there...
[Thu Jan 29 07:24:52 2015 breakdancer/lib/breakdancer-max1.4.5/] invoking kill -9 on 52630 ...
[Thu Jan 29 07:24:52 2015 breakdancer/lib/breakdancer-max1.4.5/] Closing samtools process : 52630
readgroup:MY.W.All.PE    platform:NextSeq    map:MY.W.HQ.ST_S.bam    readlen:74.99    lib:MY.W.PE    num:10000    lower:0.00    upper:464.85    mean:123.74    std:74.38    SWnormality:-54.33    flag:1(0.22%)18(57.00%)2(0.03%)20(41.84%)4(0.08%)64(0.79%)8(0.03%)14384    exe:samtools view

      Is there any mistake that I made?

      Here I'm sure there's a inversion in the result, thought the ratio is very small (~1%-5%). Can BreakDancer find it out?

      Thanks in advance!


ADD REPLYlink modified 4.6 years ago • written 4.6 years ago by Loveinheaven0
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