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Search: Posts Made By: Irsan_Kooi
Forum: Bioinformatics 09-27-2012, 12:30 PM
Replies: 1
Views: 1,432
Posted By Irsan_Kooi
That is just a tab-delimited text file with the...

That is just a tab-delimited text file with the results from breakdancer. You can import it in Excel if you change the name to BRC6.csv
Forum: Bioinformatics 09-27-2012, 12:25 PM
Replies: 4
Views: 5,318
Posted By Irsan_Kooi
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
Posted By Irsan_Kooi
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
Posted By Irsan_Kooi
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
Posted By Irsan_Kooi
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
Posted By Irsan_Kooi
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
Posted By Irsan_Kooi
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
Posted By Irsan_Kooi
I have tried to run amosvalidate on a bank made...

I have tried to run amosvalidate on a bank made from a velvet.afg file as well, no luck yet.

Does anyone know how to perform the amosvalidate on a .bnk file derived from velvet_.afg file?
Forum: Bioinformatics 07-17-2011, 12:12 PM
Replies: 7
Views: 3,912
Posted By Irsan_Kooi
I have the same problem exactly the same problem...

I have the same problem exactly the same problem as shahid.manzoor. I do velvet assembly with create .afg file option, put it in the AMOS bank, no problem. When I do amosvalidate I get the same...
Forum: Bioinformatics 06-07-2011, 05:26 AM
Replies: 65
Views: 35,825
Posted By Irsan_Kooi
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...
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