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GATB / dsk

k-mer counting software
https://gatb.inria.fr/software/dsk/
GNU Affero General Public License v3.0
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not all kmers are shown #9

Closed mamora closed 5 years ago

mamora commented 5 years ago

I run dsk to find kmer counts for a very diverse set of reads. I notice that for a 5mer only 512 5mers are shown. Some of the kmer omitted are highly present in my reads (I know that by doing a simple find-search at a text editor).

Is there any way to show a list of all kmers and their counts?

What I did so far is was running the following code with the latest dsk version:

./bin/dsk -file ./new_runs/positive_control_2_degenerate_f_r.txt.fasta -kmer-size 5

./bin/dsk2ascii -file ./new_runs/positive_control_2_degenerate_f_r.txt.h5 -out ./new_runs/positive_control_2_degenerate_f_r.txt

rchikhi commented 5 years ago

Hi, this is expected: https://github.com/GATB/dsk/blob/master/README.md#kmers-and-their-reverse-complements Actually yes, there is a way to report the count of all kmers, separating the forward and reverse complements: compile with cmake -DNONCANONICAL=1 Best, Rayan