have no peak

[JXAUDZF]

[JXAUDZF]

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

[marekkokot]

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]

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]

please download the Tibetan pig genome to make kmc

[JXAUDZF]

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]

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

[marekkokot]

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]

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

[JXAUDZF]

thanks

just like this

[JXAUDZF]

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

[JXAUDZF]

how should I do to get it?