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Fast and frugal disk based k-mer counter
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have no peak #202

Open JXAUDZF opened 2 years ago

JXAUDZF commented 2 years ago

kmer_plot6

JXAUDZF commented 2 years ago

my data is pig genome and use kmc to run fasta,but the result have not a peak.

marekkokot commented 2 years ago

Hi, are you using '-fa' or '-fm' switch? Genomes are usually in multi fasta, so '-fm' should be used. If this doesn't help show me exact command lines and give me url to download the data

JXAUDZF commented 2 years ago

have used -fm and not useful . I used the Tibetan pig genome to count . https://www.ncbi.nlm.nih.gov/data-hub/genome/GCA_000472085.2/

JXAUDZF commented 2 years ago

please download the Tibetan pig genome to make kmc

JXAUDZF commented 2 years ago

kmc -k21 -t16 -m64 -ci1 -cs10000 -fm GCA_000472085.2_2.fasta GCA_000472085.2_2 ./ kmc_tools transform GCA_000472085.2_2.fasta histogram GCA_000472085.2_2.histo -cx10000

JXAUDZF commented 2 years ago

kmc_tools transform GCA_000472085.2_2 histogram GCA_000472085.2_2.histo -cx10000

marekkokot commented 2 years ago

Hi,

well, the histogram seems to be very similar to the one get by another k-mer counting tool, so I guess the results are correct. I am not sure what exactly you expect to see in the histogram for the genome assembly dataset.

JXAUDZF commented 2 years ago

If I want to get single copy and repeat sequence peaks, do I use genome or reads data for kmer analysis

JXAUDZF commented 2 years ago

thanks

just like this

JXAUDZF commented 2 years ago

https://upload-images.jianshu.io/upload_images/27328747-7e8abc0be855d47e.png?imageMogr2/auto-orient/strip|imageView2/2/w/1200

JXAUDZF commented 2 years ago

how should I do to get it?