Question: single cell data analysis
0
gravatar for vibes1002003
11 days 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 • 141 views
ADD COMMENTlink modified 7 days ago • written 11 days 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 7 days ago • written 7 days ago by vibes100200330
1
gravatar for swbarnes2
11 days ago by
swbarnes26.5k
United States
swbarnes26.5k wrote:

Why is cellranger's aggr unsuitable for you?

ADD COMMENTlink written 11 days ago by swbarnes26.5k

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

ADD REPLYlink written 11 days ago by genomax71k
1
gravatar for Haci
11 days ago by
Haci120
Haci120 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 11 days ago by Haci120
1
gravatar for shoujun.gu
11 days ago by
shoujun.gu130
shoujun.gu130 wrote:

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

ADD COMMENTlink written 11 days ago by shoujun.gu130
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