Question: single cell data analysis
0
gravatar for vibes1002003
5 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 • 285 views
ADD COMMENTlink modified 5 months ago • written 5 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 5 months ago • written 5 months ago by vibes100200330
1
gravatar for swbarnes2
5 months ago by
swbarnes27.5k
United States
swbarnes27.5k wrote:

Why is cellranger's aggr unsuitable for you?

ADD COMMENTlink written 5 months ago by swbarnes27.5k

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

ADD REPLYlink written 5 months ago by genomax78k
1
gravatar for Haci
5 months ago by
Haci220
Haci220 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 5 months ago by Haci220
1
gravatar for shoujun.gu
5 months ago by
shoujun.gu280
shoujun.gu280 wrote:

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

ADD COMMENTlink written 5 months ago by shoujun.gu280
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