map_dna_ref: DNA mapping function

Description Usage Arguments Details Value Author(s) Examples

View source: R/map_dna_ref.R

Description

Runs the DNA mapping by Bowtie or Star

Usage

1
map_dna_ref(infile, outfile, par_list, min_hit = 5, all = FALSE)

Arguments

infile

File path to the fastq file, better controlled by parameter given by the par_list(), see set_par_list

outfile

File path to the results dir

par_list

Parameter given by the par_list(), see set_par_list

min_hit

Minimum number of reads hitting the reference [default = 5]

all

Should the reads mapped to all possible positions [default = FALSE, option of Bowtie2]

Details

The function calls the external mapper Bowtie2 or Star for the mapping. The resulting sam file is afterwards transformed to a bam file by samtools. The results are returned as an alignment data frame used later in the plot functionality.

Value

dna_alignment_df list

Author(s)

Jochen Kruppa

Examples

1

jkruppa/virDisco documentation built on May 3, 2019, 7:05 p.m.