Hi all.
I have been using HOMER for ChIP-seq analysis quite some time now for mouse samples and I absolutely love it.
However, I have been trying for the past few days to analyse some human samples and I have been having problems with the annotationPeaks.pl using the hg38 genome. The annotated peak files I am getting have only RefSeq IDs and nothing else (Unigene, Ensemble, Alias, Gene description, Gene type etc). I tried running again the annotationPeaks.pl using my own hg38.gtf file containing the gene names (gene symbols), but the only thing I managed was to substitute the RefSeq with gene symbols without any information on the rest of the columns. Does anyone know which file I should modify to get all the available information?
Any help will be very much appreciated! The empty columns are driving me crazy!
I have been using HOMER for ChIP-seq analysis quite some time now for mouse samples and I absolutely love it.
However, I have been trying for the past few days to analyse some human samples and I have been having problems with the annotationPeaks.pl using the hg38 genome. The annotated peak files I am getting have only RefSeq IDs and nothing else (Unigene, Ensemble, Alias, Gene description, Gene type etc). I tried running again the annotationPeaks.pl using my own hg38.gtf file containing the gene names (gene symbols), but the only thing I managed was to substitute the RefSeq with gene symbols without any information on the rest of the columns. Does anyone know which file I should modify to get all the available information?
Any help will be very much appreciated! The empty columns are driving me crazy!