The problem to run kmergenie

Question

[ziyingliu1996]

I am new to the RNA Seq assembly. I am trying to use velvet-Oases to do the work. To be able to determining the best K-mer, I tried to run kmergenie. However I have some problem to run kmergenie.

Thank you in advance,

the command I used as follow:

./kmergenie clipped_stillpaired1.fq clipped_stillpaired2.fq

However I got the following:

KmerGenie

Usage:
    kmergenie <read_file> [options]

Options:
    --diploid    use the diploid model
    --one-pass   skip the second pass
    -k <value>   largest k-mer size to consider (default: 121)
    -l <value>   smallest k-mer size to consider (default: 15)
    -s <value>   interval between consecutive kmer sizes (default: 10)
    -e <value>   k-mer sampling value (default: auto-detected to use ~200 MB memory/thread)
    -t <value>   number of threads (default: number of cores minus one)
    -o <prefix>  prefix of the output files (default: histograms)

I have both python and R installed.

~$ python
Python 2.7.3 (default, Feb 27 2014, 19:58:35)
[GCC 4.6.3] on linux2
Type "help", "copyright", "credits" or "license" for more information.

~$ R

R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
Copyright (C) 2013 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

... ...

Answer 1

[ziyingliu1996]

It works now.

Just create a file called "reads_file" then put all the *.fq file names into this file, each file name per line.

Then use the command as suggested in the user manuel.

Cheers,