Question: single cell data analysis
0
gravatar for vibes1002003
14 months ago by
vibes100200330
Germany
vibes100200330 wrote:

Dear all,

I am working on single cell dataset from 10x . I am trying to integrate two datasets from two different experiment but both dataset from 10x. I would like to know when integrate two datasets, the name of barcodes have an effect on tsne clustering. For integtating two datasets, what would be the best approach?

Thanks, Rahul

sequencing • 452 views
ADD COMMENTlink modified 14 months ago • written 14 months ago by vibes100200330

Thanks for the answer. I will try tools you mentioned above.

I also encounter some related to duplication of cell barcode in matrix file.
Have someone experience in this direction? Second, is it possible to combine umi tag with cellbarcode in matrix or count file fom 10x data ?

ADD REPLYlink modified 14 months ago • written 14 months ago by vibes100200330
1
gravatar for swbarnes2
14 months ago by
swbarnes29.1k
United States
swbarnes29.1k wrote:

Why is cellranger's aggr unsuitable for you?

ADD COMMENTlink written 14 months ago by swbarnes29.1k

Perhaps OP does not have access to cellranger and/or raw data? Someone else may have done the cellranger analysis.

ADD REPLYlink written 14 months ago by genomax92k
1
gravatar for Haci
14 months ago by
Haci370
Haci370 wrote:

If by "integration" you mean generating a single count table from two different datasets, you would need to add prefixes to your cell barcodes. I know that Seurat's Merge() (or sth like that) does it for you.

If you mean "aligning" datasets so as to remove batch effects, etc, you might need to check Seurat's CCA or scran's MNNCorrect. There are many more such algorithms.

ADD COMMENTlink written 14 months ago by Haci370
1
gravatar for shoujun.gu
14 months ago by
shoujun.gu310
shoujun.gu310 wrote:

No perfect merging methods. If you have to, maybe you can try MNN or scanorama.

ADD COMMENTlink written 14 months ago by shoujun.gu310
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