How do we include the actual gene name with the transcript ID from mm9 gtf?

Question

[baunruh]

Hello!

I was using homer analysis to quantify my genes in RNA-seq, which seems to have worked perfectly thus far. However when I get the homer.out file with the quantified genes it only includes the mm9 transcript ID and does not include the actual gene name. I realize I can just look up the gene name for each transcript ID but is there any way I can include this in the text file? or add it in post quantification? Just to make it easier for my lab mates to look up specific genes at a glance.

[Friederike]

which HOMER tools did you use? Based on the documentation, addGeneAnnotation.pl seems to be quite versatile and should hopefully accommodate your wishes.

[baunruh]

Hmm it doesn't appear to be working for me when I use the following:

addGeneAnnotation.pl /home/baunruh/output.txt mouse yes > output.ann.txt

for some reason it only puts the headers from the mouse file and not the actual gene names or the other annotation objects. The output.txt file I am using is the one from my previous analysis.

I mapped a file in tophat, then I used that mapped file with the same mm9 annotation and gtf file to run maketagdirectories.pl, then I used the tag directories to analyze repeats.