Re: [Breakdancer-help] Break Dancer input file

[Ken C. <kc...@wa...>]

Hi Lynnette,

     We have not tried on bam files produced by those two programs in 
combination.  Do the resulting bam files strictly follow the sam specs? 
If you are analyzing RNAseq data and the reads were mapped to the 
genomic reference, breakdancer should detect splicing as deletions.

-Ken

On 7/8/10 2:32 AM, Lynnette Fernandez wrote:
>
> Hello,
>
> I am trying to use BreakDancer in a bam file from Bowtie + TopHat 
> alignment but I am not able to create the configuration list. Is 
> Breakdancer accepting these programs?
>
> Best,
>
> Lynnette
>
> Lynnette Fernandez Cuesta, Ph.D.
> Postdoctoral fellow, Thomas Lab
> Max Planck Institute for neurological research
> Lyn...@nf...
> Tlf: 0049   0  221 4726 613
>
>
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