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Question: encode Rnaseq RPKM
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gravatar for deepaksrna
3.3 years ago by
deepaksrna • 0
Israel
deepaksrna • 0 wrote:

Hi all,

 

 Were do  i get the RPKM/CPM counts for Encode rnaseq data. Thanks
rna-seq • 912 views
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modified 3.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.3 years ago by deepaksrna • 0
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gravatar for Jennifer Hillman Jackson
3.3 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Do you mean that you wish to analyze an ENCODE dataset from scratch? Please see the tools in the group "NGS: RNA Analysis". On each tool form is a link to the 3rd party documentation outlining the different pipelines. Specific examples can be found in the Galaxy wiki - see the Galaxy NGS 101 and Learn sections to get started. 

If you are instead seeking to access results from the ENCODE project in general (such as data from a particular track), UCSC is the primary data provider: http://genome.ucsc.edu. Click on the ENCODE link to review, visualize, and download data. Most if not all datasets can be imported into Galaxy for downstream data manipulations.

If your question has been misunderstood, please provide more details so that we can try to help you.

Best, Jen, Galaxy team
ADD COMMENT • link modified 3.3 years ago • written 3.3 years ago by Jennifer Hillman Jackson ♦ 25k
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