calc_over_rep_seq: Calculate sequece counts for each unique sequence and create...
In qckitfastq: FASTQ Quality Control

Calculate sequece counts for each unique sequence and create a table with unique sequences and corresponding counts

1	calc_over_rep_seq(infile, min_size = 5L, buffer_size = 1000000L)

`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

calculate overrepresented sequence count

1 2	infile <- system.file("extdata", "10^5_reads_test.fq.gz", package = "qckitfastq") calc_over_rep_seq(infile)[seq_len(5)]

qckitfastq documentation built on Nov. 8, 2020, 5:24 p.m.

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