Hi,

Some annotations containing special characters in the gene names, for example in dm3 genome some genes have " ' '' symbol in the gene name.

Function 'read.table' in the script plot_homer_annotatepeaks.r can't properly read such files and the whole pipeline crashes in the 'merge_library_macs_qc' step. While function read.csv can process those files without problems. Guess this is because of default quote and comment char options that are different between these two functions: https://stackoverflow.com/questions/12828438/read-csv-vs-read-table

Can you please fix it?

thanks,
Anna