How to demultiplex an incomplete run using bcl2fastq2 and BCL Convert

How to demultiplex an incomplete run using bcl2fastq2

Add the use-bases-mask and ignore-missing flags to the bcl2fastq2 command to generate FastQ files from an incomplete run.

--use-bases-mask

Arguments:

N or n - Ignore the cycle.
Y or y - Use the cycle.
I or i - Use the cycle for an Index Read

For example, if a run set up is 2x100 cycles with dual 10 bp index reads and the run aborted at cycle 50 of the second read, add the following flag to demultiplex the run:

In this example, all the cycles of Read 1, all the index cycles, and 49 cycles of Read2 are used while the rest of the cycles are masked out.

Note: use one fewer cycle than completed by the run.

In addition, add the following flags as well:

--ignore-missing-bcls: The software ignores missing or corrupt BCL files and assumes 'N'/'#' for missing calls.
--ignore-missing-filter: The software ignores missing or corrupt filter files and assumes that all clusters in tiles with missing filter files passed filter.
--ignore-missing-positions: The software ignores missing or corrupt cluster location files. When cluster location files are missing, the software writes unique coordinate positions into the FASTQ header.

How to demultiplex an incomplete run BCL Convert

Add the 'OverrideCycles' setting to the settings section of a v1/v2 sample sheet to demultiplex the incomplete run.

For example, in the scenario described in the first section, add 'OverrideCycles,Y100;I10;I10;Y49N51' to the [Settings] section (v1 Sample Sheet) or [BCLConvert_Settings] section (v2 Sample Sheet) to demultiplex the run.
BCL Convert, by default, has its strict mode turned off (--strict-mode false), so missing BCL/filter/BCI/locs files do not result in the analysis erroring nor ending prematurely.
For further information, search for the Knowledge Base article How to use the 'OverrideCycles' setting with BCL Convert on BaseSpace.

Last updated 8 months ago

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