InfoPerLongRead: Combine all available information per read to a flat file

In noush-joglekar/scisorseqr: Processes long reads for differential isoform analysis

Combine all available information per read to a flat file

Description

Function to concatenate all the information per read, i.e gene-name, cellular barcode, UMI, cell-type information, and isoform information into one file. Isoform information includes a string separated list of introns, Cage and PolyA peak information if available, and a string separated list of exons. AllInfo contains the list of complete and full-length mapped, spliced, and barcoded reads. AllInfo_Incomplete is a superset of the above, and also contains reads that are not classified as complete based on Cage/PolyA data. The function also outputs basic stats such as number of reads/ genes/ UMIs per cellular barcode

Usage

InfoPerLongRead(
  barcodeOutputFile,
  mapAndFilterOut,
  minTimesIsoObserve = 5,
  rmTmpFolder = TRUE
)

Arguments

barcodeOutputFile	.csv file containing barcode and cell-type information per read from the output of GetBarcodes
mapAndFilterOut	output directory of the mapping function. If full-length reads have been filtered using CAGE and PolyA site peaks, then it defaults to that output, else it uses the canonically spliced full-length reads
minTimesIsoObserve	minimum number of times an isoform is observed in the dataset. Defaults to 5
rmTmpFolder	Logical indicating whether you want to delete contents of the pre-processing folder. Defaults to TRUE

See Also

MapAndFilter

GetBarcodes

noush-joglekar/scisorseqr documentation built on March 18, 2023, 8:06 p.m.