# BCL Convert Interactive Sample Sheet

Below you can find an interactive sample sheet with example values filled out for BCL Convert. Click on the dotted underlines for pop-ups with more information on each section.

<table data-header-hidden data-full-width="true"><thead><tr><th width="307"></th><th width="201"></th><th width="179"></th><th width="155"></th><th></th></tr></thead><tbody><tr><td><a data-footnote-ref href="#user-content-fn-1"><mark style="background-color:blue;">[Header]</mark></a></td><td></td><td></td><td></td><td></td></tr><tr><td><a data-footnote-ref href="#user-content-fn-2"><mark style="color:blue;">FileFormatVersion</mark></a></td><td>2</td><td></td><td></td><td></td></tr><tr><td><a data-footnote-ref href="#user-content-fn-3"><mark style="color:blue;">RunName</mark></a></td><td>DummyRun</td><td></td><td></td><td></td></tr><tr><td><a data-footnote-ref href="#user-content-fn-4"><mark style="color:blue;">InstrumentPlatform</mark></a></td><td>NovaSeqXSeries</td><td></td><td></td><td></td></tr><tr><td><a data-footnote-ref href="#user-content-fn-5"><mark style="color:blue;">IndexOrientation</mark></a></td><td>Forward</td><td></td><td></td><td></td></tr><tr><td><a data-footnote-ref href="#user-content-fn-6"><mark style="background-color:orange;">[Reads]</mark></a></td><td></td><td></td><td></td><td></td></tr><tr><td><a data-footnote-ref href="#user-content-fn-7"><mark style="color:orange;">Read1Cycles</mark></a></td><td>151</td><td></td><td></td><td></td></tr><tr><td><a data-footnote-ref href="#user-content-fn-8"><mark style="color:orange;">Read2Cycles</mark></a></td><td>151</td><td></td><td></td><td></td></tr><tr><td><a data-footnote-ref href="#user-content-fn-9"><mark style="color:orange;">Index1Cycles</mark></a></td><td>10</td><td></td><td></td><td></td></tr><tr><td><a data-footnote-ref href="#user-content-fn-10"><mark style="color:orange;">Index2Cycles</mark></a></td><td>10</td><td></td><td></td><td></td></tr><tr><td><a data-footnote-ref href="#user-content-fn-11"><mark style="background-color:green;">[BCLConvert_Settings]</mark></a></td><td></td><td></td><td></td><td></td></tr><tr><td><a data-footnote-ref href="#user-content-fn-12"><mark style="color:green;">SoftwareVersion</mark></a></td><td>4.1.23</td><td></td><td></td><td></td></tr><tr><td><a data-footnote-ref href="#user-content-fn-13"><mark style="color:green;">TrimUMI</mark></a></td><td>0</td><td></td><td></td><td></td></tr><tr><td><a data-footnote-ref href="#user-content-fn-14"><mark style="color:green;">Override Cycles</mark></a></td><td>Y101N50;I10;I10;N50Y101</td><td></td><td></td><td></td></tr><tr><td><a data-footnote-ref href="#user-content-fn-15"><mark style="color:green;">FastqCompressionFormat</mark></a></td><td>gzip</td><td></td><td></td><td></td></tr><tr><td><a data-footnote-ref href="#user-content-fn-16"><mark style="background-color:purple;">[BCLConvert_Data]</mark></a></td><td></td><td></td><td></td><td></td></tr><tr><td><strong>Lane</strong></td><td><strong>Sample_ID</strong></td><td><strong>index</strong></td><td><strong>index2</strong></td><td></td></tr><tr><td>1</td><td>S01-TOO-12plex-P1-rep1</td><td>ATCCACTG</td><td>AGGTGCGT</td><td></td></tr><tr><td>1</td><td>S02-TOO-12plex-P1-rep2</td><td>GCTTGTCA</td><td>GAACATAC</td><td></td></tr><tr><td>1</td><td>S03-TOO-12plex-P1-rep3</td><td>GCTTGTCA</td><td>GAACATAC</td><td></td></tr><tr><td>1</td><td>S04-TOO-12plex-P1-rep4</td><td>GCTTGTCA</td><td>GAACATAC</td><td></td></tr><tr><td><a data-footnote-ref href="#user-content-fn-17"><mark style="background-color:yellow;">[Cloud_Settings]</mark></a></td><td></td><td></td><td></td><td></td></tr><tr><td>GeneratedVersion</td><td>1.14.0.202408061842</td><td></td><td></td><td></td></tr><tr><td><a data-footnote-ref href="#user-content-fn-18">Cloud_Workflow</a></td><td>ica_workflow_1</td><td></td><td></td><td></td></tr><tr><td><a data-footnote-ref href="#user-content-fn-19">BCLConvert_Pipeline</a></td><td>urn:ilmn:ica:pipeline:d5c7e407-d439-48c8-bce5-b7aec225f6a7#BclConvert_v4_1_23_patch1</td><td></td><td></td><td></td></tr><tr><td><a data-footnote-ref href="#user-content-fn-20"><mark style="background-color:red;">[Cloud_Data</mark></a><mark style="background-color:red;">]</mark></td><td></td><td></td><td></td><td></td></tr><tr><td><strong>Sample ID</strong></td><td><strong>ProjectName</strong></td><td><strong>LibraryName</strong></td><td><strong>LibraryPrepKitName</strong></td><td><strong>IndexAdapterKitName</strong></td></tr><tr><td>Sample_001</td><td>RunName_2024-10-04T23_02_37_72dc905</td><td>Sample_001_GCCTTGTCAA_GATCCAATCA</td><td>10x3PrimeCellMultiplex</td><td>10xIndexNNSetA_3PrimeCellMultiplex</td></tr></tbody></table>

[^1]: The Header is a standalone section which provides information about the run.

[^2]: This field must exist in the header section with a value of 2 in order to identify the sample sheet as a v2 sample sheet.

[^3]: Used to capture the name of your run.

[^4]: Identifies the instrument platform to be used for the run.

[^5]: Specifies the direction you wrote your indices. If forward, the software will automatically create the reverse complement of the sequences provided for the appropriate instrument type.

[^6]: Reads is a standalone section which contains information about the read cycles and index cycles.

[^7]: Number of cycles for Read 1.

[^8]: Number of cycles for Read 2. Required only when running a paired-end sequencing run.

[^9]: Number of cycles in Index Read 1. Required if more than one sample is present in sample sheet.

[^10]: Number of cycles in Index Read 2. Required if using dual indexes for demultiplexing.

[^11]: This section contains key-value pairs that configure settings for the application, as seen in the example. The Settings section is applied globally to all samples.

[^12]: Software version of BCL Convert analysis

[^13]: If set to false or 0, UMI sequences are not trimmed from output FASTQ reads. The UMI is still placed in sequence header.

[^14]: Specifies the sequencing and indexing cycles to be used when processing the sequencing data.

    * `Y`—Specifies a sequencing read
    * `I`—Specifies an indexing read
    * `U`—Specifies a UMI cycle
    * `N`—Specifies trimmed reads

    For instruments with `RunInfo.xml`having IsReverseComplement set to `Y` for Index2, then Index2 is processed in reverse complement orientation. Apply any trimming to the end of the sequence as it transitions to the adapter, which means the N cycles specified in OverrideCycles must be in the beginning of the Index Read.

    Example of 8 bp i5 index with the last two (adapter) bases to be trimmed where XX is part of the adapter sequence.

    * Forward i5: `XXATCGCGGT`
    * ReverseComp i5: `ACCGCGATXX`(this is the direction of sequencing)
    * OverrideCycles for Index2: `N2I8`

    Although Index2 is processed on the instrument in reverse complement format, Index2 and OverrideCycles are entered in the sample sheet in forward, non-complemented format for user convenience.

[^15]: The compression format for the FASTQ output files. Example values are `gzip` or `dragen`.

[^16]: This section contains per sample data (in tabular format) used as input by the given application. The data in the first non-empty line of the application data section forms the column headers for the rest of the section. The Data section is uniquely applied to each sample.

[^17]: Specifies the analyses to be launched. Analyses to be launched can be discovered by looking in the "**Cloud\_Settings**" section for key's ending in '\_Pipeline' with string prefix \<AnalysisName> (ie, BCLConvert\_Pipeline).

[^18]: This value should always be set to ica\_workflow\_1 if doing cloud analysis. This section is not needed if doing local analysis.

[^19]: This analysis will be launched because it exists in the **Cloud\_Settings** section in the format \<AnalysisName>\_Pipeline. There must be corresponding "**\<AnalysisName>\_Settings**" and "**\<AnalysisName>\_Data**" sections present, which you can find in the rows above. This section is not needed if doing local analysis.

[^20]: This section contains data used for cloud analyses.


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