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Question: Gene name annotation
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gravatar for ghjung76
2.2 years ago by
ghjung76 • 0
ghjung76 • 0 wrote:

Hi,

I've done cufflink-> cuff merge-> cuffdiff finally, I used reference annotation human hg38 as reference gene, but I couldn't see the gene name in the file. have gene id which actually work to validate assembly in IGV though, I have a problem to get the gene name.

can you help to figure out?

Thanks, Gina
assembly cufflinks rna-seq • 772 views
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modified 2.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.2 years ago by ghjung76 • 0
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gravatar for Jennifer Hillman Jackson
2.2 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The reference GTF file must contain the attribute gene_name for this data to be promoted into the output files. iGenomes is one source of reference annotation that contains this attribute: http://support.illumina.com/sequencing/sequencing_software/igenome.html

This prior Q&A has more details, and when viewed, even more prior Q&A will appear in the right side bar. https://biostar.usegalaxy.org/p/18492/

Thanks, Jen, Galaxy team
ADD COMMENT • link written 2.2 years ago by Jennifer Hillman Jackson ♦ 25k
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