Question: readCufflinks omits gene name, ID replaced with XLOC_ ID. Any way to correct this?
0
gravatar for daniel.antony.pass
4.5 years ago by
United Kingdom
daniel.antony.pass0 wrote:

Just running through cummerbund and it's fine, other than when I have come to pinpoint particular genes, and extract the significant ones. In the gene_exp.diff and other files prior to loading into cummerbund, the information is there, but after loading the data (cuff_data <- readCufflinks('CD-LD_out')) the gene_id has been replaced with the other annotation. While parsing back is possible, I assume there's a way to use the original gene name in analysis.

 

Thanks

 

cummerbund • 1.7k views
ADD COMMENTlink modified 4.5 years ago by andrew.j.skelton73320 • written 4.5 years ago by daniel.antony.pass0
Answer: readCufflinks omits gene name, ID replaced with XLOC_ ID. Any way to correct thi
1
gravatar for andrew.j.skelton73
4.5 years ago by
United Kingdom
andrew.j.skelton73320 wrote:

Annotation in CummeRbund is not the best. You can check to see if there's any annotation:

gene.features<-annotation(genes(cuff))

What I tend to do is read in the gene and isoform tracking files as tables and use columns from that to construct a mapping from XLOC ID to annotation and TCON ID to annotation. 

ADD COMMENTlink written 4.5 years ago by andrew.j.skelton73320

Thanks, that did it.

ADD REPLYlink written 4.5 years ago by daniel.antony.pass0
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