Can ANYONE please point me in the right direction for help with DSK and GCE?
I have been able to successfully run DSK but I don't know what to do with the binary output files???
I have found some info on GCE (http://www.vcru.wisc.edu/simonlab/bioinformatics/programs/gce/README.txt.htm as well as the GCE manual) but I have no idea how to start running it? My main concern is the kmer_depth_file: is this something I need to create because it's not inside the GCE package? It also provides you with two different scripts as shown below:
gce -f test.freq [-g total_kmer_num]
./gce -f kmer_depth_file >gce.table 2>gce.log ##basic standard discrete model.
What do each of these do and which one is used for the actual run? Where do I give it my input files???
Anyone with some experience in using these software packages, please point me in the right direction?