calc_over_rep_seq: Calculate sequece counts for each unique sequence and create a table with unique sequences
and corresponding counts
Description
Calculate sequece counts for each unique sequence and create a table with unique sequences and corresponding counts
Usage
calc_over_rep_seq(infile, min_size = 5L, buffer_size = 1000000L)
Arguments
| Argument | Description |
|---|---|
infile |
A string giving the path for the fastqfile |
min_size |
An int for thhresholding over representation |
buffer_size |
An int for the number of lines to keep in memory |
Value
calculate overrepresented sequence count
Examples
r
infile <- system.file("extdata", "10^5_reads_test.fq.gz", package = "qckitfastq")
calc_over_rep_seq(infile)[seq_len(5)]