filter_reads: Filter Reads

In colbyford/cytosieve: In silico cytometric filtering of bulk sequencing data using transcriptional profiles.

Description

Filter out reads that have genes that are not expressed in a particular stage/cell type of interest. Generates a FASTQ file by filtering out reads based on a reference set of gene sequences.

Usage

filter_reads(input_path, output_path, genes_to_find = NULL,
  eliminate_matches = TRUE, pct_variability = 0.1, paired = FALSE,
  input_r2_path = NULL, output_r2_path = NULL,
  par_method = "multicore", verbose = TRUE)

Arguments

input_path	String. Path to the input .fastq file.
output_path	String. Desired path to the output filtered .fastq file.
genes_to_find	XString set of gene sequences for which to search. Usually longer sequences than the individual reads. Usually from a FASTA file.
eliminate_matches	Logical. Should the matches that are found be filtered out (TRUE) or should non-matched be filtered out (FALSE)? (Default: TRUE)
pct_variability	Numerical. The amount of variability that will be allowed in considering a match. (Default: 0.10)
paired	Logical. Should the filtering occur on both a paired forward (R1) and reverse (R2) read? If TRUE, then reads that are filtered from the R1 file will also be removed from the R2 file. (Default: FALSE)
input_r2_path	String. Path to the input (reverse) .fastq file. (Optional, only used when paired = TRUE)
output_r2_path	String. Desired path to the output (reverse) filtered .fastq file. (Optional, only used when paired = TRUE)
par_method	String. Either "multicore" for single node parallelism or "foreach" for foreach-based distribution. If "foreach" is used, then this tasks will be distributed according to the doParallel, doMPI, doSnow, etc. specifications. (Default = "multicore")
verbose	Logical. Should the process print out which read and gene it is currently searching? (Default: TRUE)

colbyford/cytosieve documentation built on April 24, 2021, 8:24 p.m.