[zhang1000]

Hi Xian:

Thank you for your information. We already saw our dataa. It is different from Illumina.
And we try to modify the original code, but failed. The results is wrong. And the author of that software still not give us response. I still wait!

Best

Jigang

[Xian]

Hi Jigang,

Which software do you mean? BreakDancer? Which email did you send the question to?

-Xian

[zhang1000]

Hi Xian:

It is breakdancer. I post my question to mail-list of breakdancer, and write a email to Dr.Chen and a sample of our data.
By the way, are you Dr.Xian Fan? If it is you, I am sorry that I did not know that. So could you please help me about our problem. Thank you so much!

Jigang

[Xian]

Hi Jigang,

I've pm'ed you.

-Xian

[ramouz87]

Hi Jigang,
Sorry for late reply,
I personnaly use IGV and tablet for viewing bam files.
Regarding the use of the data with breakdancer, I did not the time to look at that, if the bam file you are using could be made available on an ftp, i could take a look at it.
Regards,
Ramzi

[csoong]

Hello Everybody,

I am running into problem using breakdancer to find somatic rearrangements. I followed the command on the following website:

http://breakdancer.sourceforge.net/pipeline.html

However, my results are only from one "lib".
The result .ctx file has a typical line like:
chr1 121355199 5+4- chr11 51570084 25+93- CTX -525 68 3 NA2|3

Here is less-ing my config file:
readgroup:TU platform:illumina map:../cpp/0872r1_1_2_sequence.txt.sol2std.fq.sam.sort.bam.rmdup.bam readlen:100.00 lib:NA1 num:10001 lower:276.52 upper:446.96 mean:364.27 std:21.33 SWnormality:-53.69 flag:0 exe:samtools view
readgroup:NA platform:illumina map:../cpp/0871_1_2_sequence.txt.sol2std.fq.sam.sort.bam.rmdup.bam readlen:76.00 lib:NA2 num:10000 lower:313.32 upper:660.06 mean:525.81 std:43.58 SWnormality:-72.27 flag:0 exe:samtools view

Here is the output HEADER looks like:
#Software: BreakDancerMax-1.1r112
#Command: ./breakdancer_max -t -g 0872bed -d 0872pair.ctx -q 10 ../perl/0872pair.cfg
#Library Statistics:
#../cpp/0872r1_1_2_sequence.txt.sol2std.fq.sam.sort.bam.rmdup.bam mean:364.27 std:21.33 uppercutoff:446.96 readlen:100 library:NA1 reflen:3010740665 seqcov:6.00058 phycov:10.9292 32:256062
#../cpp/0871_1_2_sequence.txt.sol2std.fq.sam.sort.bam.rmdup.bam mean:525.81 std:43.58 uppercutoff:660.06 readlen:76 library:NA2 reflen:3010740665 seqcov:0.882162 phycov:3.05164 32:443164
#Chr1 Pos1 Orientation1 Chr2 Pos2 Orientation2 Type Size Score num_Reads num_Reads_lib 0871_1_2_sequence.txt.sol2std.fq.sam.sort.bam.rmdup.bam 0872r1_1_2_sequence.txt.sol2std.fq.sam.sort.bam.rmdup.bam
chr1 121484161 685+606- chr10 42398476 41+56- CTX -525 32 2 NA2|2
...
...

thank you all in advance for looking into this.

CSoong

PS: i use breakdancer_max cpp version

[findingdan]

I've noticed that bam2cfg.pl only works for some of my bam files when I use the default mapping quality but not a more lenient threshold.

perl bam2cfg.pl -q 35 s_6.pe.sorted.bam
readgroup:NA platform:illumina map:s_6.pe.sorted.bam readlen:51.00 lib:NA num:1555 lower:0.00 upper:674.20 mean:294.0std:84.74 exe:samtools view

However, using a mapping quality lower than default results in no sdout. There are reads of lower mapping quality in my bam file, and the bam file is sorted/indexed.

perl bam2cfg.pl -q 20 s_6.pe.sorted.bam
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Any ideas?

These are Illumina Ga2 PE 101bp reads, single library. No @RG info in the header.
Dan

[vyellapa]

Does BreakDancer work for Exome PE Illumina data?