> For the complete documentation index, see [llms.txt](https://knowledge.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://knowledge.illumina.com/instrumentation/general/instrumentation-general-reference_material-list/000010262.md).

# How to separate run folder BCL files by lane

**Background**

The Illumina StrataMap Spatial Transcriptome pipeline requires that the analysis be initiated from BCL files and not FASTQ files, as FASTQ files do not contain the location information necessary for analysis. When sequencing is performed by sequencing service providers using only a subset of lanes from a flowcell, the provider will need to provide only the individual project data in a way that mimics the run folder structure for subsequent analysis.

Note that this process and resulting folder is not unique to Illumina StrataMap Spatial Transcriptome data; it can be used for separating BCL files by lane for any downstream BCL Convert analysis.

**Instructions**

For analysis, the following are required to be present in the original folder structure. Therefore, they must be copied into a new folder with only the BCL files of interest.

1. BCL Files of the desired lane(s): \[run folder]/Data/Intensities/{lane, in 'L00#' format}/ or \[run folder]/Data/Intensities/BaseCalls/{lane, in 'L00#' format}
2. Positions file: in \[run folder]/Data/Intensities/s.locs
3. RunInfo.xml file: in top level of the run folder: \[run folder]/

Files can be copied manually as long as the correct folder structure is maintained.

Files can also be copied programmatically with various scripting options; an example shell script for a Linux system is provided below.

*Note that this is provided as-is as an example only, Illumina Technical Support is not able to support or help troubleshoot custom scripts or copy solutions.*

**Example shell script**

```
#!/bin/bash  

# The original BCL folder  
SRCDIR="/path/to/run_folder"  

# Where to put the new BCL folder containing only certain lanes of data  
DSTDIR="/path/to/output_folder"  

# Which lanes of data you want to separate out  
LANES=("L001" "L003")  

mkdir -p "$DSTDIR/Data/Intensities/BaseCalls"  

# Copy the RunInfo.xml  
cp "$SRCDIR/RunInfo.xml" "$DSTDIR/"  

# Copy the s.locs  
if [ -f "$SRCDIR/Data/Intensities/s.locs" ]; then  
    rsync -rv --inplace \  
        "$SRCDIR/Data/Intensities/s.locs" \  
        "$DSTDIR/Data/Intensities/"  
fi  

# Copy the Intensities and BaseCalls for the desired lanes  
for LANE in "${LANES[@]}"; do  

    if [ -d "$SRCDIR/Data/Intensities/$LANE" ]; then  
        rsync -rv --inplace \  
            "$SRCDIR/Data/Intensities/$LANE/" \  
            "$DSTDIR/Data/Intensities/$LANE/"  
    fi  

    if [ -d "$SRCDIR/Data/Intensities/BaseCalls/$LANE" ]; then  
        rsync -rv --inplace \  
            "$SRCDIR/Data/Intensities/BaseCalls/$LANE/" \  
            "$DSTDIR/Data/Intensities/BaseCalls/$LANE/"  
    fi  

done  
```

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| *For any feedback or questions regarding this article (Illumina Knowledge Article #10262), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000010262%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


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