faBuilder: fasta file builder

In XHWUlab/PolyAtailor: a toolkit for analyzing poly(A) tail length dynamics from xxx RNA-seq data

Description

faBuilder Tails and partial sequences were extracted from long reads and FASTA files were generated for alignment.

Usage

faBuilder(
  fastqfile,
  mcans,
  findUmi,
  lumi,
  adapterSeq,
  anchorSeq,
  resultpath,
  samplename,
  tailAnchorLen,
  mapping
)

Arguments

fastqfile	The path of fastqfile.
mcans	The maximum allowable mismatch number in the sliding window algorithm,default=5.
findUmi	Boolean value.Indicates whether the sequence structure contains UMI or barcode.If it is ture, the UMI or Barcode will be extracted separately.
lumi	The length of umi in reads. "lumi = 0" means there is no need to extract umi from reads.
adapterSeq	character.If you enter a FASTQ file that does not remove the 3 'adapter, please provide the full sequence of adapters.
anchorSeq	character.If your sequence structure has a sequence of anchor points identifying tails, enter this parameter.
resultpath	The path where you want to store the result data.
samplename	Specify a sample name for your data.
tailAnchorLen	Specifies the minimum tail anchor point length,default=8.
mapping	Boolean value.The default value is F.
minTailLen	Specifies the minimum tail length,default=8.

Details

This function is used to extract the PolyA tail and part of the sequence before the tail starting site from the FASTQ file containing Longread, and generate the FASTA file that can be input into the sequence alignment software.

Value

Generate a FASTA file for sequence alignment and save it to the specified directory.

See Also

[tailMap()] to quantitative tails based on sequence algin.

Other Poly(A) Tail length quantification functions: geneAnno(), tailMap(), tailScan()

Examples

fastqfile <- system.file("extdata", "./GV_fastq/PAIso_GV1.fastq", package =
"PolyAtailor", mustWork = TRUE)
faBuilderRE <- faBuilder(fastqfile,mcans=5,findUmi = F,resultpath =
"./",samplename = "GV1",tailAnchorLen=8,mapping=F)
head(faBuilderRE)

XHWUlab/PolyAtailor documentation built on Dec. 28, 2021, 12:13 a.m.