trimPrimers16S: Trim Primers from 16S Sequences (with metadata)

In claraqin/neonMicrobe: Downloading, Pre-processing, and Assembling NEON Soil Microbe Marker Gene Sequence Data

Trim Primers from 16S Sequences (with metadata)

Description

Trims primers from 16S sequences using filterAndTrim. This function assumes that each read begins with its full primer sequence and operates by truncating the beginning of each read by the length of its primer sequence.

Usage

trimPrimers16S(
  fn,
  in_subdir,
  out_subdir,
  meta,
  in_explicitdir = NULL,
  out_explicitdir = NULL,
  primer_16S_fwd = "CCTACGGGNBGCASCAG",
  primer_16S_rev = "GACTACNVGGGTATCTAATCC",
  multithread = FALSE
)

Arguments

fn	Base names of input fastq files. If inputs are not base names (i.e. if they include directory paths), the directory paths will be removed. Files that do not exist will be ignored; however, if all files do not exist, this function will issue a warning.
in_subdir	Subdirectory name from which to retrieve input fastq files. Enter "raw" for raw sequence files, or any other character string to specify a subdirectory within NEONMICROBE_DIR_MIDPROCESS/16S. To specify a directory outside NEONMICROBE_DIR_MIDPROCESS/16S, use the 'in_explicitdir' argument.
out_subdir	Subdirectory name where output fastq files will be written. Enter any character string to specify a subdirectory within NEONMICROBE_DIR_MIDPROCESS/16S. If the directory does not exist, it will be created. To specify a directory outside NEONMICROBE_DIR_MIDPROCESS/16S, use the 'out_explicitdir' argument.
meta	The output of downloadSequenceMetadata. Must be provided as either the data.frame returned by downloadSequenceMetadata or as a filepath to the csv file produced by downloadSequenceMetadata.
in_explicitdir, out_explicitdir	Directory names to use instead of 'in_subdir' and 'out_subdir', if static directory names or directories outside of NEONMICROBE_DIR_MIDPROCESS/16S are desired. Not recommended for use within processing batches.
primer_16S_fwd, primer_16S_rev	DNA sequences of 16S forward and reverse primer, respectively
multithread	Default FALSE. Whether to use multithreading. Note that Windows does not support multithreading in this function because it uses mclapply, so this argument must be set to FALSE on Windows systems.

Value

(Invisibly) Integer matrix denoting the number of reads remaining after primer-trimming for each input file.

Examples

## Not run: 
fl_nm <- c("BMI_Plate37WellA12_16S_BJ8RK_R1.fastq.gz", "BMI_Plate37WellA12_16S_BJ8RK_R2.fastq.gz")
trim_trackReads <- trimPrimers16S(
  fl_nm, in_subdir = "raw", out_subdir = "1_trimmed", meta = seqmeta_greatplains_16s,
  multithread = TRUE # set multithread = FALSE on Windows computers though
)

## End(Not run)

claraqin/neonMicrobe documentation built on April 11, 2024, 11:47 a.m.