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JiekaiLab / scTE

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gene expression from scTE were not consistent with cellranger #87

Open baishengjun opened 2 months ago

baishengjun commented 2 months ago

Hello,

I used the following commond generating the genes/TEs expression matrix and imported into scanpy to cluster, visualization. But, the gene expression generated from scTE were largely not consistent with cellranger. scTE -i inp.bam -o out -x mm10.exclusive.idx --hdf5 True -CB CB -UMI UB cellranger: image scTE image

How to explain it? or I misunderstand and make some mistake when using the scTE software?

Thanks a lot, Bai

jphe commented 2 months ago

The t-SNE layout can be used to ensure that the visualizations of both cellRanger and scTE have the same arrangement, making it easier to compare them.

In terms of the expression pattern, there are similarities between cellRanger and scTE. For the expression values in scTE are relatively smaller compared to cellRanger, this is because scRNA-seq data is based on relative quantification, where the expression values represent relative measurements rather than absolute values

cyyisbest commented 3 weeks ago

I have the same problem, the markers annotating cell types in the article have very low expression in scTE, almost none, so how should I annotate cell types?