From 10x single cell data to a bulk analysis

Question

[enho]

Hi All,

I have a 10x single cell dna sequence from a tumor which contains ~900 cells. Goal here is to look up the cells copy number.

After some analysis on the data, We realized that cells can be cluster in two clusters based on their CNV. Now we want to do some pseudo-bulk analysis on each clusters.

My question is: Is it possible to use the fastq files(output from cellranger-dna mkfastq, include I1,R1,R2 fqs) or the bam file(output from cellranger-dna cnv) to do a bulk analysis on a subset of the cells?

Even if not subseting, can a cellranger bam output file be used in a bulk pipeline? (as one sample with higher depth)

My data is: cellranger-dna mkdfastq -> Lane1-I1.fq,Lane1-R1.fq,Lane1-R2.fq,Lane2-I1.fq,Lane2-R1.fq,Lane2-R2.fq cellranger-dna cnv -> one bam file containing all the filterd reads of all the cells

Thanks