Re: [Bammds-users] Fwd: bammds

[Anna-Sapfo]

i have had that problem repeatedly but i have been able to understand 
what exactly creates the problem.
we need her header file:

output of
samtools view -H

might require a fix to the pipeline/integrate a script to convert the 
beam headers/bam files. somethiung about the order of the chromosomes, 
the sexual chromosomes etc.
anna

On 09/24/2014 05:25 PM, Ole Tange wrote:
>  From Niall's description alone I cannot solve this.
>
> I believe we support standard BAM, so my initial guess is that Niall's
> file is somehow non-standard and thus I would require an example file
> to see what goes on.
>
> Can anyone else pitch in?
>
> /Ole
>
> ---------- Forwarded message ----------
> From: OSullivan Niall <address@hidden>
> Date: Wed, Sep 24, 2014 at 11:33 AM
> Subject: bammds
>
>
> Dear Ole Tange,
>
>
>
> I am trying to use your bammds program to make a PCA plot of two
> merged shotgun programs. It asks me to change the notation and order
> of the chromosomes. I have tried to change the notation and order, but
> it results in the same error message. I would like to enquire if you
> have a script or method for converting bam files from the standard
> format to the one that is compatible with your program. I have
> searched online and been unable to find a solution.
>
>
>
> Best regards
>
>
>
> Niall
>
>
>
> --------------------------------------------------------
>
>
>
> Niall O’Sullivan, BA, MSc
>
>
>
> Researcher
>
> EURAC research
>
> Institute for Mummies and the Iceman
>
> Piazza Angela Nikoletti 14, I-39100
>
> Bolzano, Italy
>
> Tel: +39 0471 055 560
>
> Fax: +39 0471 055 579
>
> Email: address@hidden
>
>
>
> PhD candidate
>
> School of Archaeology
>
> University College Dublin
>
> Belfield
>
> Dublin 4, Ireland
>
> Email: address@hidden