Entering edit mode
6.4 years ago
baunruh
▴
10
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.
which HOMER tools did you use? Based on the documentation,
addGeneAnnotation.pl
seems to be quite versatile and should hopefully accommodate your wishes.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.