# How to generate FASTQs for a run without specifying indexes using BCL Convert

To generate FASTQs for a run using BCL Convert such that all reads from the run go to a single sample's FASTQ files (Read1 AND Read2 for paired end runs and Read 1 for single read runs):

1. Specify a single unindexed sample in the \[Data] and \[BCLConvert\_Data] sections.
2. Include the appropriate OverrideCycles settings to mask the indexes.

For example, if a 151\*10\*10\*151 run is to be processed such that all reads from the run are to go to a single sample, a suitable sample sheet for BCL Convert must include the following.

\[BCLConvert\_Settings]

OverrideCycles,Y151;N10;N10;Y151

\[BCLConvert\_Data]

Sample\_ID,index,index2,Sample\_Project

Sample\_1,,,Sample\_Project

To **create FASTQ files for the Index reads** in this scenario, include a placeholder index in the sample sheet so all reads will go to the Undetermined FASTQ files (Read1, Index1, Index2, and Read2). For the aforementioned run, a suitable sample sheet must include a pair of placeholder indexes (two polyA sequences, for instance) and no OverrideCycles, as follows.

\[BCLConvert\_Settings]

CreateFastqForIndexReads,1

\[BCLConvert\_Data]

Sample\_ID,index,index2,Sample\_Project

Sample\_1,AAAAAAAAAA,AAAAAAAAAA,Sample\_Project

As an extension, if this scenario ("unindexed" demultiplexing and indexes to be output to FASTQ files) only applies for a single lane of a run (for applicable sequencers), then a lane column must be included in the \[BCLConvert\_Settings] and \[BCLConvert\_Data] sections.

\[BCLConvert\_Settings]

CreateFastqForIndexReads,1

\[BCLConvert\_Data]

Lane,Sample\_ID,index,index2,Sample\_Project

2,Sample\_1,AAAAAAAAAA,AAAAAAAAAA,Sample\_Project

With the above example, all reads from lane 2 will be output to the 4 Undetermined FASTQ files (Read1, Read2, Index1 and Index2).

**Note**:

Starting with **BCL Convert v4.0.3**, BCL Convert has a dedicated flag, `--no-sample-sheet true`, that outputs **all reads** to a single sample called **Undetermined**.

* **Adapter trimming** and other **settings included in the sample sheet** are **ignored**, and Index FASTQ files cannot be generated with this option. The default value of this flag is False/false.

More information is available in the BCL Convert online help [page](https://support-docs.illumina.com/SW/BCL_Convert_v4.0/Content/SW/BCLConvert/BCLConvert.htm).

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| *For any feedback or questions regarding this article (Illumina Knowledge Article #7493), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000007493%20-%20Software%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


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