Im new to the ION Torrent technology and need your help to figure this out. The Ion GeneStudio™ S5 System generates BAM files as its primary output. when i need a particular FASTQ file, i can use the FileExporter plugin and get the relevant FASTQ file.
My questions are
Does the system generates a FASTQ file when generating the BAM file from WELLS file? (Illumina produce the FASTQ file as the raw data and we aligned them later)
is the generated BAM file used by FileExpoter plugin to generate the FASTQ ?
Can anyone explain the process between the WELLS file>BAM file?
FileExporter converts bam files to fastq files
Thank you for the reply. I have go through the link and found the function
which converts the BAM into a FASTQ file.
Hence FileExporter pugin uses the GATK and Picard tools.
You can convert bam file to fastq file by using Samtools
Thank you for the information. I can convert the BAM into FASTQ but i really needs to know whats happen inside the Fileexporter plugin and Torrent Basecaller.