Triplet frequencies in human genome

Question

[9606]

Hello,

does anybody know if it exists a list of nucleotide triplets associated with their frequency in the human genome (hg19 or grch38 are both ok) ?

Of course I can count it by myself, but I just wish to save some time.

[Nicolas Rosewick]

not in my knowledge. However if you need some idea to compute it : https://unix.stackexchange.com/questions/231213/count-number-of-a-substring-repetition-in-a-string

[GenoMax]

Jellyfish will do that efficiently.

Answer 1

[finswimmer]

Based on ensembl's hg38:

$ parallel -j8 "samtools faidx Homo_sapiens.GRCh38.dna.primary_assembly.fa {2} \
| seqkit seq -w0 \
| tail -n+2 \
| LC_ALL=C grep -io  {1} \
| wc -l \
| awk -v kmer={1} '{print kmer,\$0}'" ::: `echo {C,A,G,T}{C,A,G,T}{C,A,G,T}|tr " " "\n"` ::: {1..22} X Y \
| awk -v OFS="\t" 'BEGIN {print "kmer", "count"} {kmer[$1] += $2} END {for (k in kmer) {print k,kmer[k]}}' \
| sort -k1 > kmer_counts.tsv

	kmer	count
	AAA	72422544
	AAC	43498931
	AAG	58395299
	AAT	72538809
	ACA	54592537
	ACC	33744272
	ACG	7570315
	ACT	47439444
	AGA	60011989
	AGC	41032778
	AGG	51662892
	AGT	47366030
	ATA	54637885
	ATC	39037377
	ATG	53500562
	ATT	73243898
	CAA	55177058
	CAC	40478897
	CAG	59726969
	CAT	53819968
	CCA	53234309
	CCC	29406688
	CCG	8009167
	CCT	51819106
	CGA	6500298
	CGC	6757743
	CGG	8211634
	CGT	7625486
	CTA	37635012
	CTC	45987888
	CTG	58974725
	CTT	59291925
	GAA	58945303
	GAC	27703241
	GAG	46077091
	GAT	39520000
	GCA	42437940
	GCC	34453205
	GCG	6814422
	GCT	40634247
	GGA	45967975
	GGC	34430965
	GGG	29496000
	GGT	33746826
	GTA	33239299
	GTC	27434614
	GTG	40909908
	GTT	43157536
	TAA	60310660
	TAC	32854132
	TAG	37928829
	TAT	54564113
	TCA	57749469
	TCC	44865092
	TCG	6701011
	TCT	59950096
	TGA	57710783
	TGC	42118599
	TGG	54271241
	TGT	54768375
	TTA	60122345
	TTC	58852563
	TTG	56718442
	TTT	73414613

view raw triplets_hg38.tsv hosted with ❤ by GitHub

Please notice that grep matches are not overlapping. This means in case of homopolymer stretches like TTTTTT, this will be count as 2 and not 4.

[GenoMax]

seqkit is not part of standard unix install and will have to be downloaded separately.

[Nicolas Rosewick]

samtools neither ;)