readCufflinks omits gene name, ID replaced with XLOC_ ID. Any way to correct this?
1
0
Entering edit mode
@danielantonypass-7717
Last seen 8.6 years ago
United Kingdom

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 • 2.3k views
ADD COMMENT
1
Entering edit mode
@andrewjskelton73-7074
Last seen 8 days ago
United Kingdom

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 COMMENT
0
Entering edit mode

Thanks, that did it.

ADD REPLY

Login before adding your answer.

Traffic: 972 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6