Process reads to remove linker artifacts or filter by length — revmap_process • CLIPflexR

Process reads to remove linker artifacts or filter by length

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

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)