Extract allele specific matrices

SpatialTranscriptomicsResearch / st_pipeline

ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format.

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Extract allele specific matrices #116

Closed WT215 closed 4 years ago

WT215 commented 4 years ago

Hello,

I have spatial transcriptome data from mouse C57BL6 X CAST.

Can this pipeline also be used to generate allele specific gene expression matrix? So that there will be two matrices of the same dimension (gene*spot), where each element in the matrix (UMI count) correspond to cast or c57 alleles?

Thanks a lot!

jfnavarro commented 4 years ago

Hello and I apologize for the late reply.

Currently, this option is not available.

Best

WT215 commented 4 years ago

Ok I see. Thanks a lot!