4 USage
Step 1: Construct a file containing the unique k-mers specific to the gene of interest.
jellyfish count -m 29 (k-mer size) -s 100M -t 10 -C -L 1 -U 1 -o kmerdb gene.squences.fa
jellyfish will generate unique k-mers hash file
jellyfish dump kmerdb -o kmerdb.fa
Convert the binary Hash result into a text file
We provide example unique k-mer files kmerdb.faand sequenceing data test.fq, to help users quickly run.
Step 2: count the unique k-mer in sequenceing data
The output files will be saved in the current working directory
out.fq (All reads containing the input k-mer)
out_mer_count.txt (k-mer counts in sequenceing data)