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Options for Bcl Conversion and Demultiplexing

The options for demultiplexing are described below.

Option	Description	Examples
--fastq-cluster-count	Maximum number of clusters per output FASTQ file. Do not go over 16000000, since this is the maximum number of reads we recommend for one ELAND process. Specify 0 to ensure creation of a single FASTQ file. Defaults to 4000000.	--fastq-cluster-count 6000000
-i, --input-dir	Path to a BaseCalls directory.\ Defaults to current dir	--input-dir <BaseCalls_dir>
-o, --output-dir	Path to demultiplexed output. Defaults to <run_folder>/Unaligned Note that there can be only one Unaligned directory by default. If you want multiple Unaligned directories, you will have to use this option to generate a different output directory.	--output-dir <run_folder>/Unaligned
--positions-dir	Path to a directory containing positions files. Defaults depends on the RTA version that is detected.	--positions-dir <positions_dir>
--positions-format	Format of the input cluster positions information. Options: • .locs • .clocs • _pos.txt Defaults to .clocs.	--positions-format .locs
--filter-dir	Path to a directory containing filter files. Defaults depends on RTA version that is detected.	--filter-dir <filter_dir>
--intensities-dir	Path to a valid Intensities directory. Defaults to parent of base_calls_dir.	--intensities-dir <intensities_dir>
-s,--sample-sheet	Path to sample sheet file. Defaults to <input_dir>/SampleSheet.csv	--sample-sheet <input_dir>/SampleSheet.csv
--tiles	--tiles option takes a comma-separated list of regular expressions to match against the expected "s_<lane>_<tile>" pattern, where <lane> is the lane number (1-8) and <tile> is the 4 digit tile number (left-padded with 0s).	--tiles=s_[2468]_[0-9][0-9][02468]5,s_1_0001
--use-bases-mask	The --use-bases-mask string specifies how to use each cycle. • An “n” means ignore the cycle. • A “Y” (or "y") means use the cycle. • An “I” means use the cycle for the index read. • A number means that the previous character is repeated that many times. • The read masks are separated by commas "," The format for dual indexing is as follows:--use-bases-mask Y*,I*,I*,Y* or variations thereof as specified above. If this option is not specified, the mask will be determined from the 'RunInfo.xml' file in the run directory. If it cannot do this, you will have to supply the --use-bases-mask.	--use-bases-mask y50n,I6n,Y50n This means: • Use first 50 bases for first read (Y50) • Ignore the next (n) • Use 6 bases for index (I6) • Ignore next (n) • Use 50 bases for second read (Y50) • Ignore next (n)
--no-eamss	Disable the masking of the quality values with the Read Segment Quality control metric filter.	--no-eamss
--mismatches	Comma-delimited list of number of mismatches allowed for each read (for example: 1,1). If a single value is provide, all index reads will allow the same number mismatches. Default is 0.	--mismatches 1
--flowcell-id	Use the specified string as the flowcell id. (default value is parsed from the config-file)	--flowcell-id flow_cell_id
--ignore-missing-stats	Fill in with zeros when *.stats files are missing	--ignore-missing-stats
--ignore-missing-bcl	Interpret missing *.bcl files as no call	--ignore-missing-bcl
--ignore-missing-control	Interpret missing control files as not-set control bits	--ignore-missing-control
--with-failed-reads	Include failed reads into the FASTQ files (by default, only reads passing filter are included).	--with-failed-reads
--adapter-sequence	Path to a FASTA adapter sequence file. If there are two adapters sequences specified in the FASTA file, the second adapter will be used to mask read 2. Else, the same adapter will be used for all reads. Default: None (no masking)	--adapter-sequence <adapter dir>/adapter.fa
--man	Print a manual page for this command	--man
-h, --help	Produce help message and exit	-h