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Question: Cuffdiff output redundant genes
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gravatar for xusiyujune
2.5 years ago by
xusiyujune • 10
xusiyujune • 10 wrote:

Hello, I am using the Galaxy tool Cuffdiff to analyze the RNA-seq data. But for the output file "genes.fpkm_tracking", I found there are redundant genes, I mean the same gene short name, but with different tracking IDs, different gene IDs and different locus. Could you please tell me why this happen? And what's the difference between tracking IDs and gene IDs?

Thank you very much for your help. Looking forward to your reply.

rna-seq • 684 views
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modified 2.5 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.5 years ago by xusiyujune • 10
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gravatar for Jennifer Hillman Jackson
2.5 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

It sounds as if the annotation linked the gene_name with that one transcript, which then were linked with more than one gene locus. This is not uncommon for some small fraction of most datasets.

The fields are defined here: http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/index.html#fpkm-tracking-files

Best, Jen, Galaxy team
ADD COMMENT • link written 2.5 years ago by Jennifer Hillman Jackson ♦ 25k
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