Question: Any tools to count kmers in tumor/normal (contrast) pairs of samples?
2
gravatar for 14134125465346445
4.5 years ago by
United Kingdom
141341254653464453.4k wrote:

Are there any tools that would allow one to count the number of times a kmer is present in both samples of a pair of related Illumina runs? What people usually call tumor/normal or contrast kmer analysis?

I suppose there are plenty of ways to count all possible kmers present in 2 samples from k=1 to k=read length, but fewer that can do this in a reasonable amount of time and disk space.

A minimal output would be: kmer string + count sample 1 + count sample 2

ATGCGGACGCTAGCA 14 1878

ATGCGGACGCTAGC 18 1977

ATGCGGACGCTAGCG 1222 1118

...

kmer next-gen • 1.3k views
ADD COMMENTlink modified 4.5 years ago by Sean Davis25k • written 4.5 years ago by 141341254653464453.4k
1
gravatar for Sean Davis
4.5 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

A short list of kmer counting software is available here:

http://www.homolog.us/Tutorials/index.php?p=3.7&s=2

ADD COMMENTlink written 4.5 years ago by Sean Davis25k
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: 758 users visited in the last hour