R1R2toFLASH | R Documentation |
This function applies executeFLASH
over R1 and R2 reads
for multiple sample pools and returns a file with the extended reads for each pool.
R1R2toFLASH(runfiles, flash, min.ov = 20, max.ov = 300, err.lv = 0.1)
runfiles |
Vector including the paths of Illumina MiSeq Raw Data files, often with fastq.gz extension. |
flash |
File path of the FLASH executable. |
min.ov |
Minimum overlap (in nt) between R1 and R2 reads. |
max.ov |
Maximum overlap (in nt) between R1 and R2 reads. |
err.lv |
Mismatch fraction accepted in overlapping. |
The function returns a data.frame
object containing FLASH results
for sequenced regions.
After the execution, a fastq file with extended reads for each pool will be saved in a new folder named flash. Additionaly, two files will be saved in a reports folder:
FLASH_barplot.pdf
: Bar plots representing extended vs not extended reads
and the yield of the process for each pool.
FLASH_report.txt
: Includes the data returned by the function with used FLASH parameters.
Alicia Aranda
executeFLASH
runDir <- "./run" flash <- "./FLASH/flash.exe" # Save the file names with complete path runfiles<-list.files(runDir,recursive=TRUE,full.names=TRUE,include.dirs=TRUE) min.ov <- 20 max.ov <- 300 err.lv <- 0.1 flashres <- R1R2toFLASH(runfiles,flash,min.ov,max.ov,err.lv)
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