Question: I need to use BCL Convert to generate FASTQ files for my dual indexed gene expression libraries. What settings should I use in the sample sheet CSV, and will the output from the BCL Convert work with Cell Ranger?
Answer: Yes, the FASTQ files from BCL Convert will work with cellranger. There are 3 options for generating FASTQ files for any 10x library, and any of them will work fine:
If you need to use BCL Convert for gene expression libraries, these FASTQ files will work as long as they are named properly.
For running BCL Convert for gene expression libraries, here is an example sample sheet CSV that can be used:
[Header]
FileFormatVersion,2
[BCLConvert_Settings]
CreateFastqForIndexReads,0
[BCLConvert_Data]
Lane,Sample_ID,index,index2
4,PBMC_60k_Rep1,GCGGGTAAGT,CTTAGTGCTA
Here is the command to run BCL Convert:
bcl-convert \
--bcl-input-directory flowcell_input_dir \
--output-directory bcl-convert_gex \
--sample-sheet samplesheet.csv
You don't need to ouput FASTQ files for the index reads if you're demultiplexing gene expression libraries. The index reads are only needed for demultiplexing, not for Cell Ranger. If BaseSpace does not allow you to create FASTQ for index reads, that is fine for non-ATAC products.
For more information on demultiplexing ATAC and multiome ATAC libraries, the settings are different. Please see this article for more information:
Do not trim adapters for any 10x libraries. Do not include the AdapterRead1 or AdapterRead2 lines in the [BCLConvert_Settings] section. See this article explaining why:
Here are the Illumina support pages comparing compatibility between BCL Convert and bcl2fastq:
For further questions and support on BCL Convert, please contact Illumina at techsupport@illumina.com.
Related articles:
- Are the mkfastq pipelines interchangeable between products?
- Is mkfastq really needed to demultiplex, or can we use bcl2fastq?