Question: 10x genomics scRNA converting bam per cell
1
gravatar for rob.costa1234
2.8 years ago by
rob.costa1234250
United States
rob.costa1234250 wrote:

I have scRNA seq data for three time points. I ran cell ranger pipeline that gives me one bam file I want to convert this bam to one bam per sample/cell. Is there a package or toll that can help to achieve this.

rna-seq • 1.7k views
ADD COMMENTlink modified 2.8 years ago by Kevin Blighe65k • written 2.8 years ago by rob.costa1234250
0
gravatar for Kevin Blighe
2.8 years ago by
Kevin Blighe65k
Kevin Blighe65k wrote:

You may be able to do this by looking at the SAM headers, as they most likely have a sample ID (samtools view | head).

Alternatively, have you looked at what they state on 10x's website:

If you prepared multiple libraries from the same sample (technical replicates, for example), then each one should be run through a separate instance of cellranger count. Once those are completed, you can perform a combined analysis using cellranger aggr, as described in Multi-Library Aggregation. (This is illustrated in the figure).

If you prepared multiple libraries from the same sample and want to pool them and analyze the combined data as a single sample, then you will need to use the MRO syntax to treat the multiple libraries as coming from a single sample. (This is not illustrated in the figure).

[source: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger]

On the first statement, were you not able to run them separately through Cell Ranger?

ADD COMMENTlink written 2.8 years ago by Kevin Blighe65k
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