map_dna_ref: DNA mapping function
In jkruppa/virDisco: Modules for a viral detection pipeline

Description Usage Arguments Details Value Author(s) Examples

Runs the DNA mapping by Bowtie or Star

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

`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]

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.

dna_alignment_df list

Jochen Kruppa