Hello,
I am new to bioinformatics and newer to RNAseq and cummerbund. I recently ran cuffdiff on 5 samples (in triplicate). The gtf file I used did not have gene names.
The following is a line from the gtf file I used (produced by cuffmerge)
11 Cufflinks exon 100900355 100910002 . - . gene_id "XLOC_005514"; transcript_id "TCONS_00018359"; exon_number "1"; gene_name "5241"; oId "uc001pgg.2"; nearest_ref "uc001pgg.2"; class_code "="; tss_id "TSS9000"; p_id "P10682";
I would now like to add the real gene names to the cuff data set in cummerbund. I already read in the data using readCufflinks(). It appears that the addFeatures() command should accomplish what I want to do. The example suggest something like:
annot<-read.table("gene_annotation.tab",sep="\t",header=T,na.string="-")
addFeatures(cuff,annot,level="genes")
Can somebody tell me what the right format for the gene_annotation.tab should be and what the column names should be? In this case for example, I want to add "PGR" to the annotation. How will I accomplish this and how can I extract this back?
Thanks
I am new to bioinformatics and newer to RNAseq and cummerbund. I recently ran cuffdiff on 5 samples (in triplicate). The gtf file I used did not have gene names.
The following is a line from the gtf file I used (produced by cuffmerge)
11 Cufflinks exon 100900355 100910002 . - . gene_id "XLOC_005514"; transcript_id "TCONS_00018359"; exon_number "1"; gene_name "5241"; oId "uc001pgg.2"; nearest_ref "uc001pgg.2"; class_code "="; tss_id "TSS9000"; p_id "P10682";
I would now like to add the real gene names to the cuff data set in cummerbund. I already read in the data using readCufflinks(). It appears that the addFeatures() command should accomplish what I want to do. The example suggest something like:
annot<-read.table("gene_annotation.tab",sep="\t",header=T,na.string="-")
addFeatures(cuff,annot,level="genes")
Can somebody tell me what the right format for the gene_annotation.tab should be and what the column names should be? In this case for example, I want to add "PGR" to the annotation. How will I accomplish this and how can I extract this back?
Thanks