tailMap: Tail quantitative by alignment

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

Description

tailMapExtract necessary comment information from BAM files and remove IP (internal priming).

Usage

tailMap(bamfile, mcans, minTailLen, findUmi, maxNtail, mapping, longRead)

Arguments

bamfile	The path of bamfile.
mcans	The maximum allowable mismatch number in the sliding window algorithm,default=5.
minTailLen	Specifies the minimum tail length,default=8.
findUmi	Boolean value.Indicates whether the sequence structure contains UMI or barcode.If it is ture, the UMI or Barcode will be extracted separately.
maxNtail	Specifies the maximum number of tails that should be found in a sequence,default=2.
mapping	Boolean value. The default value is F.
longRead	Boolean value. If your sequence type is longreads this parameter is T, otherwise it is F, and the default is T.

Details

If your sequence is longreads, this function is used to parse BAM files, remove the IP (internal priming) from the initial tail based on the information in the cigar field in the BAM files, and finally return the dataframe with all the information of the tail.However, if your sequence type is shortreads, this function is used to extract coord annotation information from BAM files.

Value

A dataframe with all the information of the tail.Include at least read_num,tail,PAL,chr,strand,tailType,read_type and sample.

See Also

[tailScan()] to quantitative tails without sequence algin.

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

Examples

bamfile <- system.file("extdata", "./GV_algin/GV1subseq.sorted.bam", package
= "PolyAtailor", mustWork = TRUE)
GV1tailMapre<-tailMap(bamfile,mcans=5,minTailLen=8,findUmi = F,longRead=T)

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