Changes

   

   

  Output FastQ Files

  Output FastQ Files

   Output : --first [], --second [], --single []

   Output : --first [], --second [], --unpaired []

Required parameter

Required parameter

  -i InputBAM/SAM

  -i InputBAM/SAM

Optional parameters for output (however either --single or both --first and --second have to be provided)

Optional parameters for output (however either --unpaired is present or both --first and --second are provided)

  --first firstReadInAPair_FastQ

  --first firstReadInAPair_FastQ

  --second secondReadInAPair_FastQ

  --second secondReadInAPair_FastQ

Or to extract both paired end and single end fastq files (if the bam file contains both single and paired end reads)

Or to extract both paired end and single end fastq files (if the bam file contains both single and paired end reads)

   

   

   bam2FastQ -i myinput.sortByName.BAM --first myread1.fastQ --second myread2.fastQ --single myreadSingle.fastQ

   bam2FastQ -i myinput.sortByName.BAM --first myread1.fastQ --second myread2.fastQ --unpaired myreadSingle.fastQ

Or using bam (sorted or not) file to extract single end fastq files

Or using bam (sorted or not) file to extract single end fastq files

   

   

   bam2FastQ -i myinput.sortByName.BAM --single myreadSingle.fastQ

   bam2FastQ -i myinput.sortByName.BAM --unpaired myreadSingle.fastQ