bwaSampe: Generates BWA-backtrack paired-end (PE) alignments via 'bwa...

In HenrikBengtsson/aroma.seq: High-Throughput Sequence Analysis using the Aroma Framework

Description

Generates BWA-backtrack paired-end (PE) alignments via 'bwa sampe'.

Usage

## Default S3 method:
bwaSampe(pathnameSAI, pathnameFQ, indexPrefix, pathnameD, ..., verbose=FALSE)

Arguments

pathnameSAI	A character vector of two SAI files.
pathnameFQ	A character vector of two FASTQ or BAM files.
indexPrefix	The pathname prefix to the BWA index files.
pathnameD	The destination pathname.
...	Additional arguments specifying BWA 'sampe' switches passed to systemBWA().
verbose	See Verbose.

Author(s)

Henrik Bengtsson

Examples

## Not run: 
  pathnameFA <- "annotationData/organisms/Lambda_phage/lambda_virus.fa"
  bwaIndex(pathnameFA)

  pathnameSAI <- "bwaData/LambdaVirusExample/Lambda_phage/reads_1.sai"
  pathnameFQ <- "fastqData/LambdaVirusExample/Lambda_phage/reads_1.fq"
  pathnameD <- "bwaData/LambdaVirusExample/Lambda_phage/reads_1.sam"
  bwaSampe(pathnameSAI=pathnameSAI, pathnameFQ=pathnameFQ,
           pathnameFA=pathnameFA, pathnameD=pathnameD)

## End(Not run)

HenrikBengtsson/aroma.seq documentation built on Feb. 15, 2021, 2:21 a.m.