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huangyh09 / brie

BRIE: Bayesian Regression for Isoform Estimate in Single Cells
https://brie.readthedocs.io
Apache License 2.0
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Export count matrix containing isoforms #30

Closed grimwoo closed 3 years ago

grimwoo commented 4 years ago

After finishing the brie, I had three files: fractions.tsv, weights.tsv and samples.csv.gz. And I need to use Seurat for further analysis. However, I need, at least, the expression matrix. The format could be as following:

                                 AAACATACCATCAG AAACATACCGATAC AAACATACGCATCA
ENSMUSG00000111425.1               1             2              0
ENSMUSG00000024442.5               0             1              0

OR

                           Cell_1     Cell_2    Cell_3
Gene_1_isoform_1               1          2          0
Gene_1_isoform_2               0          1          0
Gene_2_isoform_1               1          1          0

Does anyone know how to export a file like this or how to combine BRIE and Seurat?

huangyh09 commented 3 years ago

Hi, Sorry on the delay. It is not straightforward to get the isoform-by-cell matrix in BRIE1, but it should be properly supported in BRIE2 (in AnnData layer).

Yuanhua