bt.bamtofastq: Convert BAM alignments to FASTQ files.
In PhanstielLab/bedtoolsr: Bedtools Wrapper

bt.bamtofastq

R Documentation

Convert BAM alignments to FASTQ files.

Convert BAM alignments to FASTQ files.

bt.bamtofastq(i, fq, fq2 = NULL, tags = NULL, output = NULL)

`i`	<BAM>
`fq`	<FQ>
`fq2`	FASTQ for second end. Used if BAM contains paired-end data. BAM should be sorted by query name is creating paired FASTQ.
`tags`	Create FASTQ based on the mate info in the BAM R2 and Q2 tags.
`output`	Output filepath instead of returning output in R.