Hello! I am doing RNA-seq analysis of human natural killer cells. I downloaded Jellyfish 2.2.6 to visualize k-mer content. The installation was the following using conda in the mac terminal (Bash):
conda install -c bioconda jellyfish
My computer is a MacBook Pro OS High Sierra version 10.13.4, by the way. And my code was the following:
gzcat reads.fastq.gz | jellyfish count -C -m 10 -s 10M
Which produces the file mer_counts.jf with the k-mer counts for k-mers of 10 bases or less. I used gzcat at the beginning because the program does not work with compressed inputs. And then, I wanted to produce an histogram that shows the frequencies of the k-mers.
jellyfish histo mer_counts.jf
but when I run this, nothing happens. No window opens, nothing. The terminal prompt comes back as if the process finished, but other jellyfish commands work. I don´t know where is the mistake... does someone notice? Thank you in advance!
I also tried to change the input part... I used gunzip -c instead of gzcat and the same happened.