Question: Nothing happens when I type jellyfish histo mer_counts.jf - command fails to produce k-mer histogram
gravatar for msimmer92
2.2 years ago by
msimmer92250 wrote:

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 donĀ“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.

rna-seq • 829 views
ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by msimmer92250

Did you check if your mer_counts.jf is empty? Did you try explicitly naming the output file:

jellyfish histo -o mer_counts.histo mer_counts.jf
ADD REPLYlink written 2.2 years ago by h.mon30k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1539 users visited in the last hour