tailScan: Use a variety of methods to help you quantify the tails in a...

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

Description

tailScan Returns a table containing at least read_num, tail length, and tail sequence.

Usage

tailScan(
  fastq,
  mcans,
  findUmi,
  lumi,
  adapterSeq,
  anchorSeq,
  resultpath,
  samplename,
  tailAnchorLen,
  minTailLen,
  realTailLen,
  maxNtail,
  mapping,
  mapinfo
)

Arguments

fastq	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.
minTailLen	Specifies the minimum tail length,default=8.
realTailLen	Specifies what you think is the true tail length,default=30.
maxNtail	Specifies the maximum number of tails that should be found in a sequence,default=2.
mapping	Boolean value.The default value is F.

Details

This function quantifies the possible tails of all sequences in a FASTQ file with a non-aligned manner.You need to specify the parameters according to the structure of your sequence.We will save the found tail data and the sequence data that did not find the tail to the path you specified

Value

Save the quantitative tail results table of various algorithms to the path you specify.Meanwhile, return the tail dataframe

See Also

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

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

Examples

fastqfile <- system.file("extdata", "./GV_fastq/PAIso_GV1.fastq", package =
"PolyAtailor", mustWork = TRUE)
GV1tailDF<-tailScan(fastqfile,mcans=5,findUmi = F,resultpath =
"./",samplename =
"GV1",tailAnchorLen=8,minTailLen=8,realTailLen=20,maxNtail=2,mapping=F)
head(GV1tailDF)

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