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Question: Gz Files
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gravatar for Keith E. Giles
8.7 years ago by
Keith E. Giles • 170
United States
Keith E. Giles • 170 wrote:
I apologize for the redundancy, I sent the previous email from the wrong account. I am trying to figure out why I can't upload the .gz compressed files from the broad institute into galaxy. any suggestions?
galaxy • 1.0k views
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modified 7.4 years ago by Jennifer Hillman Jackson ♦ 25k • written 8.7 years ago by Keith E. Giles • 170
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gravatar for Rohan Sachdeva
8.7 years ago by
Rohan Sachdeva • 10
Rohan Sachdeva • 10 wrote:
You probably have to unarchive it and then upload the raw seq files.
ADD COMMENT • link written 8.7 years ago by Rohan Sachdeva • 10
It is possible to directly upload gzipped files - they will be gunzipped upon upload. This is a good way to upload large data that comrpesses well. Keith, can you provide more information? Does Galaxy provide any error messages when this occurs? Thanks, --nate
ADD REPLY • link written 8.7 years ago by Nate Coraor ♦ 3.2k
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gravatar for Eccles, David
7.7 years ago by
Eccles, David • 10
Eccles, David • 10 wrote:
to tell R to analyse each SNP one after the other? I would also advise using plink for this. Calculating SNP marker statistics [1] is the one of the things that it has been designed to do. The main problem is getting data into a format supported by plink, either linkage (one line per individual), or transposed pedigree (one line per marker). There are details on these formats in the plink documentation [2]. [1] http://pngu.mgh.harvard.edu/~purcell/plink/summary.shtml#freq [2] http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#tr -- David Eccles (gringer)
ADD COMMENT • link written 7.7 years ago by Eccles, David • 10
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gravatar for Jennifer Hillman Jackson
7.4 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
Hello Curtis, Please see under "Shared Data" in the public Galaxy for examples that cover a range of analysis. For RNA-seq, this tutorial will likely be helpful (under "Shared Data -> Published Pages -> Galaxy RNA-seq Analysis Exercise"): http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise Thanks! Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org/ http://galaxyproject.org/
ADD COMMENT • link written 7.4 years ago by Jennifer Hillman Jackson ♦ 25k
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