[Bio-Linux] tophat with -p > 1 results in missing reads

[Josh Thackray]

Hi Tim,

As I posted on the tophat github issue tracker 
(https://github.com/infphilo/tophat/issues/18), it looks like the 
upgrade solved the problems I was having. Thanks very much for your help!

Just as an aside, I don't receive replies to my messages on the email 
list (though I do receive the digest emails). Is there any way to fix this?

Thanks,

Josh

Josh Thackray
Laboratory Researcher III
Human Genetics Institute of NJ
Department of Genetics
Rutgers University

On 9/2/2015 7:00 AM, bio-linux-request at nebclists.nerc.ac.uk wrote:
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> Today's Topics:
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>     1. Re: Portable biolinux not booting in Dell inspiron 3000
>        (Tim Booth)
>     2. Re: tophat with -p > 1 results in missing reads (Tim Booth)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 01 Sep 2015 12:41:38 +0100
> From: Tim Booth <tbooth at ceh.ac.uk>
> To: Bio-Linux help and discussion <bio-linux at nebclists.nerc.ac.uk>
> Subject: Re: [Bio-Linux] Portable biolinux not booting in Dell
> 	inspiron 3000
> Message-ID: <1441107698.5600.56.camel at wllt1771.nerc-wallingford.ac.uk>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi Bish,
>
> Your image of the error seems to have been eaten by the mailing list
> server.  Could you please paste it onto pasteboard.co (or somewhere
> similar) and send the link?
>
> There can be issues with UEFI and Linux but this is normally because of
> flaky UEFI implementations and Dells should behave themselves so I think
> it should be possible to achieve what you want and get it to boot
> reliably.  From your description I can't tell if the error regarding
> USB-3 is coming from Grub or from the Kernel.  Hopefully when I see the
> screenshot image it will be clear.
>
> Once I can see where in the boot process the error is occurring I think
> we can use the Gateway laptop to fix the system on the drive.  If you
> plug the external drive into your Gateway it boots right up, right?  If
> so, things we can do are:
>
> 1) Disable the boot logo and reveal all the diagnostic messages
> 2) Force Grub to load all relevant drivers
> 3) Rebuild the initrd to ensure the kernel properly starts the USB3
> stack before mounting the root filesystem
> 4) Upgrade the kernel to the "utopic" or "vivid" backport version.  I
> can't do this on the regular ISO because it stuffs up VirtualBox client
> driver support, but it might well fix your problem.
>
> Anyway, post up the image and we'll go from there.
>
> Cheers,
>
> TIM
>
> On Tue, 2015-09-01 at 14:31 +0530, Duleep Samuel wrote:
>> I would suggest that you use virtualbox and use biolinux, UEFI boot
>> has problems with Linux, Samuel, IIHR, Bangalore
>>
>> On Fri, Aug 28, 2015 at 9:15 PM, Bishwa Kiran
>> <kirannbishwa01 at gmail.com> wrote:
>>          I have been trying to install a portable bio-linux OS on
>>          external hdd. I have followed the instructions given for
>>          portable ubuntu/bilinux installation which has been sucessful
>>          and also made sure the boot/grub loader is installed in the
>>          external harddrive (seagate 2 tb) during installation. After
>>          the completion of bio-linux installation it requests the
>>          restart and biolinux boots up. But, after the 2nd boot the
>>          boot widow of biolinux gives me an error (that a USB-3 port is
>>          not available or is offline). I have installed biolinux
>>          several times thinking the installation may have missed the
>>          files but it always turns out the same way- 1st restart works
>>          but after the second restart/boot there is an error message.
>>          My desktop is Dell inspiron 3000 (i3) which by default uses
>>          UEFI boot system and I have disabled it while preparing the
>>          biolinux installation and have used legacy mode (modified BIOS
>>          setting).
>>          One interesting thing is that the same portable biolinux OS
>>          which didn't boot from desktop boots from my gateway laptop
>>          every time though. So, the problem basically is that the USB-3
>>          port is not getting recognized while booting. I tried another
>>          USB-3 port which gave same error, all other  USB 2 port
>>          however show biolinux OS loading (shows a loading Biolinux
>>          logo) but never fully boots even after 2-3 hours.
>>          
>>          
>>          I have been trying to make this work for 5 days now. I need to
>>          use this portable OS mainly on my desktop due it its higher
>>          performance and also I have to keep things running overnight.
>>          Any suggestions appreciated and thanks in advance.
>>          
>>          
>>          I took the picture of the error message.
>>          
>>          
>>          --
>>          - Bish
>>           
>>          
>>           
>>          
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>>
>>
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