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Re: [Bammds-users] Fwd: bammds

From: Anna-Sapfo
Subject: Re: [Bammds-users] Fwd: bammds
Date: Wed, 24 Sep 2014 17:46:08 +0200
User-agent: Mozilla/5.0 (X11; Linux x86_64; rv:31.0) Gecko/20100101 Thunderbird/31.1.1

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.

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?


---------- 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 O’Sullivan, BA, MSc


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


Dublin 4, Ireland

Email: address@hidden

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