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Question: analyse the data form the CCLE(cghub)
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gravatar for heming_wang
2.8 years ago by
heming_wang • 20
heming_wang • 20 wrote:

Hi

I download the a RNA seq data(Aligned) from the cghub browser.

The format of the file is the bam, and the study is CCLE.

But I cannot analyse the data , what should I do before I use this bam format data?

Thank you!
rna-seq galaxy • 896 views
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modified 2.8 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.8 years ago by heming_wang • 20
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gravatar for Jennifer Hillman Jackson
2.8 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The BAM dataset was uploaded successfully in a Galaxy server (local, cloud, public - was this http://usegalaxy.org)? Use FTP since the file is likley over 2G. Only load the .bam. A new .bam.bai is created upon upload.

Here are some examples for how-to: https://wiki.galaxyproject.org/Support#Loading_data

If there are problems, please explain what they are specifically. If tools are not recognizing it the input, double check the datatype assignment and potentially the database attribute (reference genome) and assign if missing. Click on the pencil icon per-dataset to do this, or these attributes can be assigned all at once during upload in that form. 

Please share more details addressing some of the questions above, if this is not enough help. Jen, Galaxy team
ADD COMMENT • link written 2.8 years ago by Jennifer Hillman Jackson ♦ 25k
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