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>
> 




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