bwaSamse: Generates BWA-backtrack single-end (SE) alignments via 'bwa...

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

Description

Generates BWA-backtrack single-end (SE) alignments via 'bwa samse'.

Usage

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

Arguments

pathnameSAI	The SAI file to be aligned.
pathnameFQ	The FASTQ file to be aligned.
indexPrefix	The pathname prefix to the BWA index files.
pathnameD	The destination pathname.
...	Additional arguments specifying BWA 'samse' 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"
  bwaSamse(pathnameSAI=pathnameSAI, pathnameFQ=pathnameFQ,
           pathnameFA=pathnameFA, pathnameD=pathnameD)

## End(Not run)

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