Question: Does Jellyfish support zipped fastq sequences?
0
gravatar for comma1993
2.2 years ago by
comma19930
comma19930 wrote:

I used jellyfish to counting kmers and my input files were zipped fastq. I used the commond :

jellyfish count -m 17 -o 17mer_counts -s 500000000 -t 5 -c 3 read_1.fq.gz read_2.fq.gz

And I got the errors like this:

terminate called after throwing an instance of 'std::runtime_error'
  what():  Unsupported format

I don't know how to solve it.

kmer assembly genome • 1.9k views
ADD COMMENTlink modified 2.2 years ago by genomax71k • written 2.2 years ago by comma19930

Answer to your question is no. Workaround is described by @Sej below.

ADD REPLYlink written 2.2 years ago by genomax71k
5
gravatar for Sej Modha
2.2 years ago by
Sej Modha4.4k
Glasgow, UK
Sej Modha4.4k wrote:

Jellyfish manual: http://www.genome.umd.edu/docs/JellyfishUserGuide.pdf

2.1 How to read compressed files (or other format) Jellyfish only reads FASTA or FASTQ formatted input files. By reading from pipes, jellyfish can read compressed files, like this: zcat *.fastq.gz | jellyfish count /dev/fd/0 ... or by using the '<()' redirection provided by the shell (e.g. bash, zsh): jellyfish count <(zcat file1.fastq.gz) <(zcat file2.fasta.gz) ...

ADD COMMENTlink modified 2.2 years ago by WouterDeCoster41k • written 2.2 years ago by Sej Modha4.4k

Thanks for your reply~~It helps a lot.

ADD REPLYlink written 2.2 years ago by comma19930
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