I am working with a 10x Genomics workflow on a NextSeq 550 instrument. Unfortunately, I don't have a sample sheet, but I do have a run report with the following information:
Sample Specie LibraryType ExpGroup Index RunID
Lib_DDM_05 Mus musculus scRNA-seq 3’ NextGEM v3.1 SI-GA-A1 201002_NB552055_0122_AH2FWKBGXG
Lib_DDM_06 Mus musculus scRNA-seq 3’ NextGEM v3.1 SI-GA-B1 201002_NB552055_0122_AH2FWKBGXG
The files I have are:
Base call files (*bcl.bgzf)
Base call index files (*.bci)
Filter files (*.filter)
Cluster location files (*.locs)
RunInfo.xml
[Optional] Sample sheet (*.csv) #- which I don't have
Given this situation, how can I proceed with converting BCL files to FASTQ using bcl2fastq? Any guidance or detailed instructions would be greatly appreciated.
Thank you!
1 answer
You should use cellranger (which in turn uses bcl2fastq, so you will need both) to do this demultiplexing. Doing this would translate the SI-GA-* codes automatically without you having to create elaborate samplesheets. The process is described here: https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/inputs/cr-mkfastq
You can create a simple samplesheet for cellranger as described on the page above.
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