Hello Yitian,

On 12/23/13 7:12 PM, Yitian Xu wrote:
Hi Galaxy,

I am a user from Cornell University. And you website is a great help to me and my research. But there are two problems with it I cannot figure out by myself, hoping you can help me.

1. When I uploading the data via FTP, there's option of mouse reference genome mmp10. When I get to Tophat2, there's only mmp9. Is there a problem that I use mmp10 at the beginning and use mmp9 at tophat2? Or maybe you will update the tophat2?
mm10 will be added as an indexed genome for Bowtie2/Tophat2 in the near term.

It is very important to use the same version of a genome for all steps in an analysis, otherwise the chromosomes and/or coordinates will not match up. If doing RNA-seq analysis, the reference genome used for mapping and the reference annotation (GTF/GFF3 file) should all be the same. Ideally, you will want the input fastq sequences also labeled as this same reference genome to stay organized, but this is optional.

More RNA-seq help is here:
https://wiki.galaxyproject.org/Support#Tools_on_the_Main_server:_RNA-seq
And the iGenomes reference GTF file for mm9 is already loaded as a shared dataset, if you wish to use it, under "Shared Data -> Data Libraries -> iGenomes".


2. I have around 50G space missing. I have one and only one history (at least I can see) with 171.5G, but when I checked my preference I used 225.2G. I don't know where the missing 50G count for then I don't know how to make room for my ongoing analysis. My user name is douyadou. Can you help me check for a min?
It may be that you have deleted, but not permanently deleted, histories or datasets. This wiki explains how to check:
https://wiki.galaxyproject.org/Learn/Managing%20Datasets#Delete_vs_Delete_Permanently
We will also examine your account for administrative issues and get back to you if any anomalies are found.

Thank you!

Jen
Galaxy team

Thanks.

Best,
Yitian


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The Galaxy User list should be used for the discussion of
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