25 March 2020
QuicKmer2 files for the mouse genome, mm10

Files included:
[jmkidd@gl-login2 mm10]$ ls -lh ref/
total 66G
-rw-rw-r-- 1 jmkidd kiddlab 2.6G Mar 25 18:23 mm10.fa
-rw-rw-r-- 1 jmkidd kiddlab  88M Mar 25 18:21 mm10.fa.bed
-rw-rw-r-- 1 jmkidd kiddlab 2.5K Mar 25 18:23 mm10.fa.fai
-rw-rw-r-- 1 jmkidd kiddlab 3.9G Mar 25 18:24 mm10.fa.qgc
-rw-rw-r-- 1 jmkidd kiddlab  49G Mar 25 18:23 mm10.fa.qm
-rw-rw-r-- 1 jmkidd kiddlab  74K Mar 25 18:23 toInclude.bed

Cmd used to generate:
QuicK-mer2/quicKmer  search -k 30 -t 20 -s 3G -e 2 -d 100 -w 1000 -c ref/toInclude.bed ref/mm10.fa

Regions that were excluded include:
segmental duplications (UCSC genome browser track)
Variant regions from Yalcin et al (PMID: 22439878) lifted over to mm10
CNV regions in founder strains from Morgan et al (PMID: 28592499, table S7)
Non-primary and non-autosomal chromosomes (chrX, chrY, chrM, chrUn*, chr*_random)

Converted to regions to include using bedtools

Total output 2051106346 k-mers