Forum: Bioinformatics
09-27-2012, 12:30 PM
|
|
Replies: 1
Views: 1,432
|
|
Forum: Bioinformatics
09-27-2012, 12:25 PM
|
|
Replies: 4
Views: 5,318
That is definetely not the problem. With...
That is definetely not the problem. With breakdancer you can specify multiple .bam files. It just piles them up and uses all the reads together and in the end for each called structural variant it...
|
|
Forum: Bioinformatics
07-23-2012, 10:17 AM
|
|
Replies: 1
Views: 3,549
Hi Bair,
I am having the same problem. Using...
Hi Bair,
I am having the same problem. Using breakdancer the output consists of DEL, INV, INS, CTX and ITX. Though breakdancer tries to support detection of somatic variants I don't think it is...
|
|
Forum: Bioinformatics
07-16-2012, 01:00 AM
|
|
Replies: 5
Views: 4,048
Hey all,
I found out that when you want to...
Hey all,
I found out that when you want to do a tumor normal SV-detection with breakdancer you need to be sure that your have the read group information in your bam-file set. To check if that is...
|
|
Forum: Bioinformatics
06-27-2012, 09:06 AM
|
|
Replies: 2
Views: 1,459
Hi there,
I have the same situation,...
Hi there,
I have the same situation, illumina paired end reads, have run breakdancer and want to compare results with pemer. I think i have managed to get it to work, it is running now for half a...
|
|
Forum: Bioinformatics
06-15-2012, 08:00 AM
|
|
Replies: 5
Views: 4,048
Hi there Karin and Catch,
I have the same...
Hi there Karin and Catch,
I have the same questions as you. Right now, I am pursuing the same strategy as karin to find out the answer (run breakdancer on tumor and normal sample seperately and...
|
|
Forum: Bioinformatics
06-15-2012, 07:48 AM
|
|
Replies: 1
Views: 1,385
Hi there,
I just ran breakdancer on a single...
Hi there,
I just ran breakdancer on a single sample...
[myprompt]$ breakdancer_max -d breakdancer_HelaOM20_ HelaOM20.cfg > SV_breakdancer_HelaOM20.ctx
So something else is happening
Irsan
|
|
Forum: Bioinformatics
07-17-2011, 12:24 PM
|
|
Replies: 5
Views: 5,381
|
|
Forum: Bioinformatics
07-17-2011, 12:12 PM
|
|
Replies: 7
Views: 3,912
|
|
Forum: Bioinformatics
06-07-2011, 05:26 AM
|
|
Replies: 65
Views: 35,825
Does anyone have an idea how long it takes to...
Does anyone have an idea how long it takes to perform a single end assembly with CLC assembly cell 3.2.2. on 24 Gbases of data using quadcore with 16 GB or RAM.
P.S. I know what they claim on the...
|
