#' Generate genome index for bowtie
#' @importFrom glue glue
#' @param fasta_path fasta file containing reference sequences to be aligned for
#' @param index_name Name of the index
#' @export
glue_bowtie_genome_generate <-
function(fasta_path, index_name){
glue("
bowtie-build -f {fasta_path} {index_name}
")
}
#' Map with bowtie and output a sorted bam file
#' @importFrom glue glue
#' @param head_label .tar file path
#' @param index_name .tar file path
#' @param core_num number of threads to use
#' @param in_dir .tar file path
#' @param out_dir .tar file path
#' @export
glue_bowtie_bamsort <-
function(
head_label,
index_name,
in_dir = "./fastq",
out_dir = "./mapped_by_bowtie",
core_num = 2
){
lineend <- "\\"
fq_ext <- fq_ext
glue(
"
mkdir {out_dir}
bowtie {lineend}
-p {core_num} {lineend}
-S {lineend}
-a --best --strata {line_end}
{index_name} {lineend}
{in_dir}/{head_label}.{fq_ext} {lineend}
| {lineend}
samtools view -@ {core_num} -bS {lineend}
| {lineend}
samtools sort -@ {core_num} > {out_dir}/{head_label}.sort.bam
samtools index {out_dir}/{head_label}_bowtie.sort.bam
"
)
}
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