demultiplex bcl files from 10X genomics and generate fastq file for each sample separately

Question

[Sara]

I have bcl files from 10X genomics and trying to demultiplex them and generate fastq files. to do so, I m using cellranger mkfastq and once I have fastq files I will use cellranger multi. for the cellranger mkfastq command I need to specify --samplesheet or --csv file. according to the website of 10X genomics, the format of that file if we have multiple library types, looks like this:

Lane,Sample,Index
1,GEX_sample,SI-TT-D9
1,CMO_sample,SI-NN-A1

and I need to make a file almost like this since I also have multiple library types. but in our case, we have pulled the cells from different conditions and we want to have data from different conditions in a separate fastq file. once we demultiplexed the bcl files but we got all the reads from all samples in 2 fastq files (R1 and R2 which means like they are the same sample). how can I ask the program or make a new samplesheet or csv file, to have the reads from different conditions in separate fastq files?

[GenoMax]

You need to make and provide the samplesheet to cellranger. Have you looked at https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/mkfastq where the process is explained with examples.

since I also have multiple library types

I don't know what you mean by that. Do you have samples from more than one type e.g. single cell RNAseq and ATACseq?