Question: List all solid k-mers with DSK
1
gravatar for alexandre.drouin.8
2.1 years ago by
alexandre.drouin.810 wrote:

Hi,

I am using DSK to count the k-mers that are present in multiple fasta files. I would like to get the list of all solid k-mers that were found in all files.

The command line interface has a "-solid-kmers-out" argument which, I assume, should output this list in a file. However, even when I set a value, it does not seem to output a file. Am I using it correctly?

Also, is there a programmatic way to go from the integer representation of k-mers to their string representation?

Thanks for your help, Alex

dsk • 781 views
ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by alexandre.drouin.810
3
gravatar for Rayan Chikhi
2.1 years ago by
Rayan Chikhi1.3k
France, Lille, CNRS
Rayan Chikhi1.3k wrote:

Bonjour Alexandre,

To output the solid kmers in string representation, you can either use the dsk2ascii tool provided with DSK, or parse the hdf5 file using h5dump. See https://github.com/GATB/dsk#results-visualization

To integrate DSK results in a C++ program, it is currently recommended to use the GATB-core library. Have a look at the doxygen page and also the example code in the GATB-core repository that demonstrate some custom processing:

  • kmer10.cpp is the most up to date version of that snippet.
  • kmer16.cpp shows how to get separate kmer counts (one abundance per file) over multiple files (multi-bank kmer counting)
  • kmer11-15 are a bit more advanced

Thanks for pointing this out by the way, the "-solid-kmers-out" argument was actually made for GATB-core graph construction (to output the graph and the solid kmers in different files), and is not used in DSK. I've added a note for the future versions of DSK.

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by Rayan Chikhi1.3k
0
gravatar for alexandre.drouin.8
2.1 years ago by
alexandre.drouin.810 wrote:

Merci Rayan! I will have a look at the snippets.

Alex

ADD COMMENTlink written 2.1 years ago by alexandre.drouin.810
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 901 users visited in the last hour