The run name format is:

Side A: <date>_AV240903_<name>_A

Side B: <date>_AV240903_<name>_B

Sample sheet (run manifest)

Instructions to prepare the sample sheet (manifest): https://docs.elembio.io/docs/run-manifest/

Demultiplexing via Bases2Fastq

Instructions to set up Bases2Fastq software https://docs.elembio.io/docs/bases2fastq/setup/

The command for the demultiplexing:

./bases2fastq input output -p 8 -r samplesheet

The command structure:

• ./bases2fastq invokes the installed static binary executable.

• input defines the path to the input run directory.

• output defines the path to the output directory. Running twice with the same output directory overwrites the location.

• -p threads Bases2Fastq for faster parallel execution. The value depends on your system setup. The example command has a value of 8, which requires at least 8 CPUs.

• -r the sample sheet path

For example:

bases2fastq /data/av240903/AV240903/<run name>/ /data/fastq/<run name> -p 8  -r /data/fastq/<run name>/<sample sheet file name>

For more details https://docs.elembio.io/docs/bases2fastq/running-bases2fastq/

 For lane separated use --split-lanes

Add Lane column in the sample sheet

The command:

./bases2fastq /input /output --split-lanes

For ATAC-seq

./bases2fastq input output -p 8 -r samplesheet --settings 'UmiMask,I2:Y*' --legacy-fastq