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?
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.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?