CellTagExtraction: CellTag Extraction Function
In morris-lab/CloneHunter: Identify Clonal Identity from ScRNA-Seq and CellTag Data

Description Usage Arguments Value Examples

This function extracts CellTags from the raw fastq/bam sequencing file. If it is a fastq file, provides counts of each CellTag and sorts them in desending order. If it is a bam file, returns the barcode, umi, celltag information.

1 2	CellTagExtraction(fastq.bam.input, celltag.version, extraction.output.filename, save.fullTag = TRUE, save.onlyTag = TRUE)

`fastq.bam.input`	The input fastq/bam data directory
`extraction.output.filename`	The output file directory, i.e. where would you like to store the 8nt tags with their counts?
`save.fullTag`	Would you like to save full sequences with the short sequences provided without counts? Defaults to TRUE
`save.onlyTag`	Would you like to save only the 8nt CellTags without counts? Defaults to TRUE
`short.nt.before.tag`	A short sequence before the 8nt tag to help more specific identification
`short.nt.after.tag`	A short sequence after the 8nt tag to help more specific identification

A list contains count table of CellTags. If requested to save fullTag counts, i.e. save.fullTag.counts = TRUE, return a list of both 8nt tags and full sequences count. Otherwise, a list of 8nt tags counts.