read_hexamer.py¶

Calculate hexamer (6-mer) frequency from read sequences and optionally compare to a reference genome or transcriptome.

Usage¶

read_hexamer.py -i reads.fq

Options¶

Option	Description	Default
`-i`, `--input`	Read sequences in FASTA or FASTQ format. Multiple files separated by `,`	Required
`-r`, `--refgenome`	Reference genome sequence in FASTA format	Optional
`-g`, `--refgene`	Reference mRNA sequences in FASTA format	Optional

Output¶

Prints tab-separated hexamer frequencies to stdout. Columns include the hexamer sequence and observed frequency, plus reference frequencies if provided.