align: align

In robinweide/tagmeppr: A computational pipeline to map tagmap-insertions

Description

Align reads on the hubrid reference genome.

Usage

align(exp, ref, cores = 20, dedup = T, empericalCentre = F,
  BWA_path = NULL, samtools_path = NULL, verbose = F)

Arguments

exp	The tagMeppr-object of a sample.
ref	A reference object of makeIndex or loadIndex.
cores	The number of threads used in the mapping-stage.
dedup	Remove suspected PCR-duplicates?
empericalCentre	The location of the center of the inserted sequence in the transposon.fa. This is needed to find the orientation of the insertion. Can be T, F or numeric: TRUE Will find it automatically FALSE Will take the middle of the transposon.fa. This doesn't have to be the case when you loaded a BAC containing the insertion. numeric Will use this number as the postion of the middle.
BWA_path	A string to the complete BWA-path.
samtools_path	A string to the complete samtools-path.
verbose	Do you want a more chatty function?

Value

The object will be updated with the following slots:

alignmentFolder

The path to the folder of BAM-files

insertName

The name of the transposon in the hybrid reference

seqinfo

The seqinfo of the hybrid reference

FWDBAM

GenomicAlignments of the mapping of forward reads

REVBAM

GenomicAlignments of the mapping of reverse reads

alignedReadsFWD

Granges-oject with informative forward reads

alignedReadsREV

Granges-oject with informative reverse reads

insertionMid

The used position of the middle of the insertion

Author(s)

Robin H. van der Weide, [e-mail]

Examples

## Not run: 
reference_hg19_PB = makeIndex(indexPath = '/home/A.Dent/analysis42/',
                              bsgenome = 'BSgenome.Hsapiens.UCSC.hg19',
                              ITR = 'PiggyBac')

C9 = newTagMeppr(F1 = 'clone9_FWD_R1.fq.gz',
                 F2 = 'clone9_FWD_R2.fq.gz',
                 R1 = 'clone9_REV_R1.fq.gz',
                 R2 = 'clone9_REV_R2.fq.gz',
                 name = "clone9",
                 protocol = 'PiggyBac')

align(exp = C9, ref = reference_hg19_PB, cores = 30, empericalCentre = T)

## End(Not run)

robinweide/tagmeppr documentation built on Feb. 26, 2020, 10:41 p.m.