Sort error while running Cuffdiff

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Sort error while running Cuffdiff

TD
Hi All --

I'm a novice when it comes to all things programming, but I recently installed my own instance of Galaxy because I'm working with very large datasets. Everything seems to be running OK, but when I attempt to run Cuffdiff (w/ ref. annotation and bias correction from UCSC genome) on output from Tophat2, I get the following error: "Error: sort order of reads in BAMs must be the same." I'm perplexed, because I downloaded this output from Tophat2 that I ran on the public server, before putting it through Cuffdiff on my local instance. When I tried running the same files (prior to download) in Cuffdiff on the public server, they ran just fine.

So, why do the files run properly when I run them publicly, but not locally? Am I missing some metadata? Is my install not complete? Does the ordering of bam files change when you download them? I've had a hard time finding solutions, so any tips are greatly appreciated.

Cheers!

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Re: Sort error while running Cuffdiff

Johnson, Nathan T. (MU-Student)

Any luck?  Running into the same issue as well.




TD <Todd.Dembo@...> writes:

>
>
> Hi All --
>
>
> I'm a novice when it comes to all things programming, but I recently
installed my own instance of Galaxy because I'm working with very large
datasets. Everything seems to be running OK, but when I attempt to run
Cuffdiff (w/ ref. annotation and bias correction from UCSC genome) on output
from Tophat2, I get the following error: "Error: sort order of reads in BAMs
must be the same." I'm perplexed, because I downloaded this output from
Tophat2 that I ran on the public server, before putting it through Cuffdiff
on my local instance. When I tried running the same files (prior to
download) in Cuffdiff on the public server, they ran just fine.
>
> So, why do the files run properly when I run them publicly, but not
locally? Am I missing some metadata? Is my install not complete? Does the
ordering of bam files change when you download them? I've had a hard time
finding solutions, so any tips are greatly appreciated.
>
> Cheers!
>
>
> <div><div dir="ltr">
> <div class="gmail_default">Hi All --</div>
> <div class="gmail_default"><br></div>
> <div class="gmail_default">
> I'm a novice when it comes to all things programming, but I recently
installed my own instance of Galaxy because I'm working with very large
datasets. Everything seems to be running OK, but when I attempt to run
Cuffdiff (w/ ref. annotation and bias correction from UCSC genome) on output
from Tophat2, I get the following error: "Error: sort order of reads in BAMs
must be the same." I'm perplexed, because I downloaded this output from
Tophat2 that I ran on the public server, before putting it through Cuffdiff
on my local instance. When I tried running the same files (prior to
download) in Cuffdiff on the public server, they ran just fine.</div>
> <div class="gmail_default"><br></div>
> <div class="gmail_default">So, why do the files run properly when I run
them publicly, but not locally? Am I missing some metadata? Is my install
not complete? Does the ordering of bam files change when you download them?
I've had a hard time finding solutions, so any tips are greatly appreciated.
</div>
> <div class="gmail_default"><br></div>
> <div class="gmail_default">Cheers!</div>
> </div></div>
>




___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
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