Question: Cuffcompare results in an empty file
gravatar for jasvinder.kaur
2.8 years ago by
jasvinder.kaur0 wrote:


I am trying to run cuffcompare on a cuffmerge file using local galaxy but i am getting an empty output with an error that reference genome not present. I am using the locally cached human reference genome in the parameters. Can anyone please suggest what could I be possibly doing wrong. I don't have much experience with RNA Seq analysis so suggestions will be really appreciated!



ADD COMMENTlink modified 2.8 years ago by Jennifer Hillman Jackson25k • written 2.8 years ago by jasvinder.kaur0
gravatar for Jennifer Hillman Jackson
2.8 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Did you install the genome using a Data Manager from the Tool Shed? It sounds as if either the .len data or possibly another key index (samtools) is not present. On a local, be sure to use the Data Manager for installing a genome with a dbkey if it is not already in the default list. Then also create a 2bit, Samtools, and Picard index as the first steps before creating the Tophat indexes. If you need to start over, just use a slightly different dbkey for the genome.

Removing indexes that are already installed is very difficult (and manual). However, if the older index really needs to be removed, (in many cases not, instead consider just a adding a new one), it is recommended to instead start over with a fresh Galaxy instance, then install indexes using the correct data managers, in this order.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.8 years ago by Jennifer Hillman Jackson25k
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