From farhat.habib at gmail.com  Wed Mar  9 09:24:31 2011
From: farhat.habib at gmail.com (Farhat Habib)
Date: Wed, 9 Mar 2011 19:54:31 +0530
Subject: [Bio-Linux] Error while updating
Message-ID: <AANLkTinep9=_yJJV=c-Z_AxoWDAx4P9pxw+UC4Fb94DE@mail.gmail.com>

Dear All,

On trying to update using the Package manager I am running into this error.


W: GPG error: http://nebc.nerc.ac.uk unstable Release: The following
signatures were invalid: BADSIG B1A598E8128B92BD NEBC Team (Bio-Linux 6
package signing key) <helpdesk at nebc.nox.ac.uk>
W: A error occurred during the signature verification. The repository is not
updated and the previous index files will be used.GPG error:
http://www.stats.bris.ac.uk lucid/ Release: The following signatures were
invalid: BADSIG 51716619E084DAB9 Michael Rutter <marutter at gmail.com>

What should I do?

Thanks,
-Farhat

--
Farhat Habib, PhD
Scientist-C, Center of Excellence in Epigenetics
Indian Institute of Science Education & Research,
Sai Trinity Building, Garware Circle,
Sutarwadi, Pashan, Pune-411 021.
http://www.iiserpune.ac.in/~farhat
Twitter: @far_hat
Office: +91 20 2590 8080
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From makson96 at gmail.com  Wed Mar  9 09:53:51 2011
From: makson96 at gmail.com (Tomasz Makarewicz)
Date: Wed, 9 Mar 2011 15:53:51 +0100
Subject: [Bio-Linux] Error while updating
In-Reply-To: <AANLkTinep9=_yJJV=c-Z_AxoWDAx4P9pxw+UC4Fb94DE@mail.gmail.com>
References: <AANLkTinep9=_yJJV=c-Z_AxoWDAx4P9pxw+UC4Fb94DE@mail.gmail.com>
Message-ID: <AANLkTimoADFwf4Z1-hvSYFhRKo06gnc2ZDpedQTSSeUN@mail.gmail.com>

http://lmgtfy.com/?q=ubuntu+gpg+error

2011/3/9 Farhat Habib <farhat.habib at gmail.com>

> Dear All,
>
> On trying to update using the Package manager I am running into this
> error.
>
>
> W: GPG error: http://nebc.nerc.ac.uk unstable Release: The following
> signatures were invalid: BADSIG B1A598E8128B92BD NEBC Team (Bio-Linux 6
> package signing key) <helpdesk at nebc.nox.ac.uk>
> W: A error occurred during the signature verification. The repository is
> not updated and the previous index files will be used.GPG error:
> http://www.stats.bris.ac.uk lucid/ Release: The following signatures were
> invalid: BADSIG 51716619E084DAB9 Michael Rutter <marutter at gmail.com>
>
> What should I do?
>
> Thanks,
> -Farhat
>
> --
> Farhat Habib, PhD
> Scientist-C, Center of Excellence in Epigenetics
> Indian Institute of Science Education & Research,
> Sai Trinity Building, Garware Circle,
> Sutarwadi, Pashan, Pune-411 021.
> http://www.iiserpune.ac.in/~farhat
> Twitter: @far_hat
> Office: +91 20 2590 8080
>
>
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>
>


-- 
http://ubuntu.pl
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From mashanovvlad at googlemail.com  Wed Mar  9 09:59:09 2011
From: mashanovvlad at googlemail.com (vladimir mashanov)
Date: Wed, 9 Mar 2011 10:59:09 -0400
Subject: [Bio-Linux] Error while updating
In-Reply-To: <AANLkTinep9=_yJJV=c-Z_AxoWDAx4P9pxw+UC4Fb94DE@mail.gmail.com>
References: <AANLkTinep9=_yJJV=c-Z_AxoWDAx4P9pxw+UC4Fb94DE@mail.gmail.com>
Message-ID: <AANLkTimEmeHjc9GcHWfVb_HmzHXyJkh5V7kvR1GSg-xx@mail.gmail.com>

Dear Farhat,

I had the same problem too. Below is the reply from Tim Booth that
helped in my case:

The README should answer your question:

http://cran.r-project.org/bin/linux/ubuntu/README


Best,

Vladimir.

On 9 March 2011 10:24, Farhat Habib <farhat.habib at gmail.com> wrote:
> Dear All,
> On trying to update using the Package manager I am running into this error.
>
> W: GPG error: http://nebc.nerc.ac.uk unstable Release: The following
> signatures were invalid: BADSIG B1A598E8128B92BD NEBC Team (Bio-Linux 6
> package signing key) <helpdesk at nebc.nox.ac.uk>
> W: A error occurred during the signature verification. The repository is not
> updated and the previous index files will be used.GPG error:
> http://www.stats.bris.ac.uk lucid/ Release: The following signatures were
> invalid: BADSIG 51716619E084DAB9 Michael Rutter <marutter at gmail.com>
> What should I do?
> Thanks,
> -Farhat
> --
> Farhat Habib, PhD
> Scientist-C, Center of Excellence in Epigenetics
> Indian Institute of Science Education & Research,
> Sai Trinity Building, Garware Circle,
> Sutarwadi, Pashan, Pune-411 021.
> http://www.iiserpune.ac.in/~farhat
> Twitter: @far_hat
> Office: +91 20 2590 8080
>
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>
>



-- 
Vladimir Mashanov, PhD
Universidad de Puerto Rico
Faculdad de Ciencias Naturales
Departamento de Biologia
JGD Building, #220
PO Box 70377, UPR Station
Rio Piedras, PR 00936-8377
email: mashanovvlad at googlemail.com;
vladimir.mashanov at uprrp.edu


From farhat.habib at gmail.com  Wed Mar  9 10:08:02 2011
From: farhat.habib at gmail.com (Farhat Habib)
Date: Wed, 9 Mar 2011 20:38:02 +0530
Subject: [Bio-Linux] Error while updating
In-Reply-To: <AANLkTimoADFwf4Z1-hvSYFhRKo06gnc2ZDpedQTSSeUN@mail.gmail.com>
References: <AANLkTinep9=_yJJV=c-Z_AxoWDAx4P9pxw+UC4Fb94DE@mail.gmail.com>
	<AANLkTimoADFwf4Z1-hvSYFhRKo06gnc2ZDpedQTSSeUN@mail.gmail.com>
Message-ID: <AANLkTik+4=HPcX0=fMHB9+Dc5cceNcU=ocKzvbfb1Ev0@mail.gmail.com>

Many thanks!

-Farhat

--
Farhat Habib, PhD
Scientist-C, Center of Excellence in Epigenetics
Indian Institute of Science Education & Research,
Sai Trinity Building, Garware Circle,
Sutarwadi, Pashan, Pune-411 021.
http://www.iiserpune.ac.in/~farhat
Twitter: @far_hat
Office: +91 20 2590 8080



On Wed, Mar 9, 2011 at 8:23 PM, Tomasz Makarewicz <makson96 at gmail.com>wrote:

> http://lmgtfy.com/?q=ubuntu+gpg+error
>
> 2011/3/9 Farhat Habib <farhat.habib at gmail.com>
>
>> Dear All,
>>
>> On trying to update using the Package manager I am running into this
>> error.
>>
>>
>> W: GPG error: http://nebc.nerc.ac.uk unstable Release: The following
>> signatures were invalid: BADSIG B1A598E8128B92BD NEBC Team (Bio-Linux 6
>> package signing key) <helpdesk at nebc.nox.ac.uk>
>> W: A error occurred during the signature verification. The repository is
>> not updated and the previous index files will be used.GPG error:
>> http://www.stats.bris.ac.uk lucid/ Release: The following signatures were
>> invalid: BADSIG 51716619E084DAB9 Michael Rutter <marutter at gmail.com>
>>
>> What should I do?
>>
>> Thanks,
>> -Farhat
>>
>> --
>> Farhat Habib, PhD
>> Scientist-C, Center of Excellence in Epigenetics
>> Indian Institute of Science Education & Research,
>> Sai Trinity Building, Garware Circle,
>> Sutarwadi, Pashan, Pune-411 021.
>> http://www.iiserpune.ac.in/~farhat
>> Twitter: @far_hat
>> Office: +91 20 2590 8080
>>
>>
>> _______________________________________________
>> Bio-Linux mailing list
>> Bio-Linux at nebclists.nerc.ac.uk
>> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>>
>>
>
>
> --
> http://ubuntu.pl
>
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>
>
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From tbooth at ceh.ac.uk  Wed Mar 30 12:55:28 2011
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Wed, 30 Mar 2011 17:55:28 +0100
Subject: [Bio-Linux] FastQC tool for checking high throughput sequence data
Message-ID: <1301504128.1947.3814.camel@barsukas>

Hi All,

Today we've been playing with the FastQC tool from the Babraham
institute.  It takes the .fastq file you get from an Illumina run and
makes some nice reports and graphs to let you visualise various metrics
for your sequences and assess the quality.

Downloading and running the tool is fairly easy but I've made a
Bio-Linux package that comes with the added convenience of an icon
appearing in the Bioinformatics menu, so you may want to use that
instead:

apt-get install bio-linux-fastqc

We had some 454 data to analyse and it was saved as separate .fasta
and .qual files which needed to be converted to a single .fastq file for
FastQC.  If you need to do the same, there are some handy conversion
scripts now on the website:

http://nebc.nerc.ac.uk/tools/code-corner/scripts/sequence-formatting-and-other-text-manipulation

Cheers,

TIM

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://nebc.nerc.ac.uk
+44 1491 69 2705

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