revmap_process: Process reads to remove linker artifacts or filter by length
In kathrynrozengagnon/CLIPflexR: CLIP tools and wrappers in R

revmap_process

R Documentation

Process reads to remove linker artifacts or filter by length

Description

Process reads to remove linker artifacts or filter by length

Usage

revmap_process(fastas, linkers = NULL, length_max = NULL, length_min = NULL)

Arguments

`fastas`	path to FASTA file to process.
`linkers`	contaminating sequences to remove, default is NULL, set to character string to specify.
`length_max`	maximum length required during fasta processing, default is NULL, set to integer to specify.
`length_min`	minimum length required during fasta processing, default is NULL, set to integer to specify.

Value

path to processed FASTA.

Author(s)

Kathryn Rozen-Gagnon

Examples

testFastq <- system.file("extdata/SRR1742056.fastq.gz",package="CLIPflexR")
FqFile <- decompress(testFastq,overwrite = TRUE)
FaFile <- fastx_qtoa(FqFile)
processed_Fa <-  revmap_process(FaFile, linkers="GGACGATGC", length_min=18, length_max=30)

kathrynrozengagnon/CLIPflexR documentation built on Dec. 8, 2022, 7:31 p.m.