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Question: RNA seq analysis for samples from TCGA.
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gravatar for smn5360
3.6 years ago by
smn5360 • 10
Brunei Darussalam
smn5360 • 10 wrote:

I got files RNA seq files from TCGA. They are in TAR archive and will extract them. How do I upload them into Galaxy to analyse. My aim is to analyse the expression level of different transcription factors in  relation to BRCA one samples in breast cancer

Yesterday I tried to upload the file from my computer but showed error.
rna-seq software error galaxy • 1.8k views
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modified 3.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.6 years ago by smn5360 • 10

I am working on a project for PSU term project. Need help.

ADD REPLY • link written 3.6 years ago by smn5360 • 10

Do we normalised data from TCGA or result file to upload into GALAXY

ADD REPLY • link written 3.6 years ago by smn5360 • 10
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gravatar for Jennifer Hillman Jackson
3.6 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Archives in ".tar" format are not an accepted input format. Most other compression types are. So, untar then load the data. More Upload help is here. These options work at http://usegalaxy.org and most other public Galaxy servers:
http://wiki.galaxyproject.org/Support#Loading_data

If you are on a local (this wasn't clear), FTP would need to be enabled to use that. Plus you have the option of loading from the file system into Data Libraries. Help for these are in the "Admin" section of the wiki:
http://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles
http://wiki.galaxyproject.org/Admin/Config/UploadviaFTP

Best, Jen, Galaxy team
ADD COMMENT • link modified 3.6 years ago • written 3.6 years ago by Jennifer Hillman Jackson ♦ 25k

Thanks. I did manage to upload files in tabular format from TCGA. The data comes in different types, normalised data, result file,exon quantification.  Since they are normalised do I just change format to fastQ, groom, and then do cufflinks. DO I still need to do the Tophat

What should I do at this point. I also want to see differential expression of Transcription factors doing RNA seq analysis.

Can I do a Needle and Water on it to see conservation along diffrent samples.

I have around 75 samples and want to put it in a comparable matrix.

 

ADD REPLY • link written 3.6 years ago by smn5360 • 10
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