This function applies
FastqStreamer over a fastq file and removes
all reads that have a defined fraction of bases below Q30. The remaining reads will be saved
in a new fastq file.
FiltbyQ30(max.pct = 0.05, flashfiles, flashres, ncores = 1)
The maximum percentage of bases below Q30 allowed in reads (by default,5%).
Vector including the paths of files that are going to be processed, with fastq extension.
Table of results obtained after the execution of
Number of cores to use for parallelization with
This function is designed to be applied after
R1R2toFLASH function from
the same package. If
flashres is not specified but FLASH extension was previously
done, the function will try to load the FLASH results table from the reports folder.
data.frame object containing FLASH and Filtering results. This results
table includes two new columns with respect to FLASH results table, named FiltQ30 (number of filtered reads)
and Raw (total sequencing reads).
After the execution, a fastq file with remaining reads for each pool will be saved in a new flashFilt folder (if it is not previously created). Additionaly, two report files will be generated in a reports folder:
FiltQ30.barplot.pdf: Includes a first Bar plot representing raw reads,
extended reads by FLASH and filtered reads, and a second Bar plot with
the yield by process for each pool.
FiltQ30_report.txt: Includes the same data frame returned by the function
containing FLASH and Filtering results.
runDir <- "./run" runfiles <- list.files(runDir,recursive=TRUE,full.names=TRUE,include.dirs=TRUE) flash <- "./FLASH/flash.exe" flashDir <- "./flash" flashfiles <- list.files(flashDir,recursive=TRUE,full.names=TRUE,include.dirs=TRUE) flashres <- R1R2toFLASH(runfiles,flash) filtres <- FiltbyQ30(max.pct=0.05,flashfiles,flashres)
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