Sort error while running Cuffdiff
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!
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
<div class="gmail_default"><br></div> <div class="gmail_default">So, why do the files run properly when I run
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> 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>
participants (2)
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Nathan T. Johnson -
TD