run_bowtie | R Documentation |
Runs the bowtie tool, currently set up primarily to get unaligned reads
run_bowtie(
input1 = NULL,
input2 = NULL,
index = NULL,
sample.name = NULL,
out.dir = NULL,
unaligned = NULL,
format = "SAM",
parallel = FALSE,
cores = 4,
execute = TRUE,
bowtie = NULL,
version = FALSE
)
input1 |
List of the paths to files containing to the forward reads, required |
input2 |
List of the paths to files containing to the reverse reads, required for paired end sequence data |
index |
Path to the reference transcriptome kallisto index, required |
sample.name |
List of the sample names, required |
out.dir |
Name of the directory from the Bowtie output. If NULL, which is the default, a directory named "bowtie_alignments" is created in the current working directory. |
unaligned |
Name of the directory for the unaligned reads, fastq formatted |
format |
Format for the aligned reads, currently only SAM is supported |
parallel |
Run in parallel, default set to FALSE |
cores |
Number of cores/threads to use for parallel processing, default set to 4 |
execute |
Whether to execute the commands or not, default set to TRUE |
bowtie |
Path to the bowtie proram, required |
version |
Returns the version number |
A list with the bowtie commands
## Not run:
bowtie.path <- "/software/bowtie-v1.2.3/bin/bowtie"
bowtie.version <- run_bowtie(bowtie = bowtie.path,
version = TRUE)
trimmed_reads_dir <- "trimmed_reads"
input1 <- list.files(path = trimmed_reads_dir, pattern = "*_R1_001.fastq$", full.names = TRUE)
index <- "path/to/index/indes.ebwt"
sample_names <- unlist(lapply(strsplit(list.files(path = trimmed_reads_dir,
pattern = "*_R1_001.fastq$",
full.names = FALSE),"_"), `[[`, 1))
unaligned <- "rRNA_removed_reads"
out.dir <- "/dev/null" # Send the reads that align to be deleted
bowtie.cmds <- run_bowtie(input1 = mate1,
index = index, sample.name = sample_names,
unaligned = unaligned,
out.dir = out.dir,
bowtie = bowtie.path)
## End(Not run)
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