Question: Attributes required for cuffdiff annotation file
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gravatar for bdeonovic
6.3 years ago by
bdeonovic180
United States
bdeonovic180 wrote:

I want to use cufflinks to do differential expression analysis (8 samples, 4 cases, 4 controls). I have a reference annotation file (refFlat.gtf). In the manual for cuffdiff it states that cuffdiff requires certain attributes (i.e. tss_id, p_id) and that those can be added to the annotation file using the command

    cuffcompare -s /path/to/genome_seqs.fa -CG -r annotation.gtf annotation.gtf

When I run this command I get a lot less lines in my annotation file:

[bdeonovic@neon-login-0-2 stoltz]$ wc -l cuffcmp.combined.gtf 
35768 cuffcmp.combined.gtf


[bdeonovic@neon-login-0-2 stoltz]$ wc -l refFlat.gtf 
78642 refFlat.gtf

Is this necessary? Is there a way to append these cufflink annotations without merging together my gene annotations? 

rna-seq cuffdiff cufflinks • 1.8k views
ADD COMMENTlink modified 6.3 years ago by Biostar ♦♦ 20 • written 6.3 years ago by bdeonovic180
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