assignSRAreads: Assign SRA reads for desposited 10X single cell RNAseq...

View source: R/GetSRAreads.R

assignSRAreadsR Documentation

Assign SRA reads for desposited 10X single cell RNAseq datasets

Description

This function takes an input directory containing fasterq-dump or fastq-dump files. Fasterq and fastq outputs must be generated from using the split option. Example: fasterq-dump –include-technical –split-files or fastq-dump –split-files PLEASE NOTE This will not take the output of fasterq/fastq-dump if you specified the –type argument

Usage

assignSRAreads(
  working_dir = NULL,
  input_dir = NULL,
  outdir = NULL,
  parallel = FALSE
)

Arguments

working_dir

Set working directory. Provide absolute paths

input_dir

Set to directory containing fasterq-dump or fastq-dump files

outdir

Directory to output the read legnths as SRRXXXXX_X.readlength.txt

parallel

if TRUE, uses mclapply from parallel package. default=FALSE

Details

250 reads from all fastq files are then sampled from the listed fastqs and assigned to R1, R2 or I3. 10,000 reads will also be sampled if the reads are matched for R1

Value

A dataframe containing SRR_ID, assigned_read, orig_names, new_names and cellranger_names A csv will be written into the outdir "assigned_SRAreads.csv".


Nusob888/fasterqParseR documentation built on March 11, 2024, 2:48 p.m.