480
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchno edit summary
Output FastQ Files
Output FastQ Files
Output : --first [], --second [], --single []
Output : --first [], --second [], --single []
Required parameter
-i InputBAM/SAM
Optional parameters for output (however either --single or both --first and --second have to be provided)
--first firstReadInAPair_FastQ
--second secondReadInAPair_FastQ
--single unpairedReads_FastQ
In order to extract paired end reads, the BAM file has to be sorted by name, e.g. using samtools. Suppose the BAM file is myinput.bam
samtools sort -n myinput.bam myinout.sortByName.bam
Using sorted bam file to extract paired end fastq files
bam2FastQ -i myinput.sortByName.BAM --first myread1.fastQ --second myread2.fastQ
Or to extract both paired end and single end fastq files
bam2FastQ -i myinput.sortByName.BAM --first myread1.fastQ --second myread2.fastQ --single myreadSingle.fastQ
Or using bam (sorted or not) file to extract single end fastq files
bam2FastQ -i myinput.sortByName.BAM --single myreadSingle.fastQ
