How to Convert 10x BCL Files to FASTQ Without a Sample Sheet Using Only Run Report Information?

Question

[Divya]

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!

[Ram]

Of all the "tags" you used, bcl2fastq was the only relevant, subject-matter related one. Please don't use non subject-matter phrases and multi-word descriptors as tags, stick to sensible subject matter keywords.

Answer 1

[GenoMax]

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.

[Divya]

Thankyou so much for your valuable response