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Re: [Bammds-users] bammds
From: |
OSullivan Niall |
Subject: |
Re: [Bammds-users] bammds |
Date: |
Thu, 25 Sep 2014 14:39:56 +0000 |
Hi
I think it may be the reference file that was used for the bwa mapping. I used
HG19 and I downloaded it directly from UCSC. You used a different one, but from
where?
Best wishes
Niall
-----Original Message-----
From: address@hidden [mailto:address@hidden On Behalf Of Ole Tange
Sent: mercoledì 24 settembre 2014 16.12
To: address@hidden
Cc: OSullivan Niall
Subject: Fwd: bammds
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
To: "address@hidden" <address@hidden>
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
- [Bammds-users] Fwd: bammds, Ole Tange, 2014/09/24
- [Bammds-users] Fwd: bammds, Ole Tange, 2014/09/24
- Re: [Bammds-users] bammds,
OSullivan Niall <=
- Re: [Bammds-users] bammds, Ole Tange, 2014/09/25
- Re: [Bammds-users] bammds, OSullivan Niall, 2014/09/25
- Re: [Bammds-users] bammds, Anna-Sapfo, 2014/09/26
- Re: [Bammds-users] bammds, OSullivan Niall, 2014/09/26
- Re: [Bammds-users] bammds, José Víctor Moreno Mayar, 2014/09/26
- Re: [Bammds-users] bammds, Anna-Sapfo, 2014/09/30
- Re: [Bammds-users] bammds, OSullivan Niall, 2014/09/30