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Question: Gene ID from chromosome locus - Cufflinks/Cuffdiff outputs plus other data formats
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gravatar for nadia.shouman13
8 months ago by
nadia.shouman13 • 0
nadia.shouman13 • 0 wrote:

Hello,

Can anyone help me in how to get the gene ID out of gene locus on galaxy?

Thank you,
rna-seq gtf gene_name cufflinks cuffdiff • 310 views
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modified 8 months ago by Jennifer Hillman Jackson ♦ 25k • written 8 months ago by nadia.shouman13 • 0
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gravatar for Jennifer Hillman Jackson
8 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

For mapping coordinates to genes (any data), this prior Q&A covers how-to: https://biostar.usegalaxy.org/p/11833/

For Cufflinks/Cuffmerge/Cuffdiff data:

  • If the reference annotation (GTF) supplied to Cufflinks already contains the gene_name attribute, you can use the tool Cut to isolate the value.

  • If the GTF used didn't have this attribute, consider using a GTF that does have it (iGenomes is one choice). Details are in a prior Q&A post (and those linked from it): https://biostar.usegalaxy.org/p/19615/

  • Many more posts about this are in other prior Q&A and can be reviewed/search for in the sidebar of similar posts >>>

  • AND if you would rather avoid all of this extra processing - and use improved RNA-seq analysis methods - you could switch to using the latest tools. See the Galaxy tutorials here for example workflows: https://galaxyproject.org/learn/

Thanks! Jen, Galaxy team
ADD COMMENT • link modified 8 months ago • written 8 months ago by Jennifer Hillman Jackson ♦ 25k
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