Question: Nothing happens when I type jellyfish histo mer_counts.jf - command fails to produce k-mer histogram
gravatar for msimmer92
19 months ago by
msimmer92210 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 • 623 views
ADD COMMENTlink modified 19 months ago • written 19 months ago by msimmer92210

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 19 months ago by h.mon28k
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