I'm trying to use Bcl2Fastq to convert raw BCL files into fastq files from a paired-end targeted sequencing run on an Illumina MiSeq. I'm able to run Bcl2fastq in a linux server environment without getting any errors - the program is able to locate all of the BCL files, and the filepaths for the created fastq files are displayed in the shell window as the program runs. However, when I list the files in the output directory (where the resultant fastq files should appear), I am unable to find them, and they don't seem to actually have been created. Has anyone else run into this problem with bcl2fastq?
Thanks,
Max
You need to redirect the output to a file using the '>' symbol to specify redirection
i.e. bcl2fastq myfile.bcl > my file.fastq
Note: when you do this, it won't display to the screen.
Illumina MiSeq sequencer suppose to create fastq files by default. Please check the sequencer for the fastq files..
Alternatively it is helpful, if you can share the version of bcl2fastq you are using and the command.
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