Question: Kmer and rev-comp in separate nodes
1
gravatar for Shatlyk Ashyralyyev
2.2 years ago by
Turkey
Shatlyk Ashyralyyev20 wrote:

Hi,

I've just started learning the basics of GATB. Not sure if it is meaningful, but I have a simple question:

Is it possible to force to create two separate nodes for a kmer and its reverse complement, instead of merging them into a single node with minimum value?

Shatlyk.

gatb • 675 views
ADD COMMENTlink modified 2.2 years ago by edrezen690 • written 2.2 years ago by Shatlyk Ashyralyyev20
1
gravatar for edrezen
2.2 years ago by
edrezen690
France
edrezen690 wrote:

Hello,

No, GATB does not allow to have two distinct nodes for a kmer and its reverse complement.

ADD COMMENTlink written 2.2 years ago by edrezen690

Thanks!

Any advices on how to find the amount of abundance of a node that appeared in input sequences as kmer itself (not as its reverse complement)? Or do we lose this information?

ADD REPLYlink written 2.2 years ago by Shatlyk Ashyralyyev20

Yes, GATB loses this information currently. A kmer and its reverse complement are considered to be the same object.. If this is blocking for you, i.e. you would use GATB if it supported counting kmers and reverse complement separately, write me at rayan@gatb.fr

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by Rayan Chikhi1.2k
1

No, it does not block me now. Actually, I'm trying to grasp the basics of GATB, in order to figure out what should I add on top of GATB to use in my project. Thank you very much, for the help!

ADD REPLYlink written 2.2 years ago by Shatlyk Ashyralyyev20
1
gravatar for edrezen
2.2 years ago by
edrezen690
France
edrezen690 wrote:

Ok, my answer was focused more on the de Bruijn graph than on the kmers abundances.

Strange enough, we never considered for GATB the possibility to count kmers as they appeared in input sequences, maybe because we were interested in creating de Bruijn graphs where a node holds both a kmer and its reverse complement.

However, I just tried some hack in the GATB code and it is indeed possible to count kmers the way you want. We will think about the way to cleanly include this hack in a future version of GATB because this may be interesting for other people as well.

 

 

 

ADD COMMENTlink written 2.2 years ago by edrezen690
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