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cistrome / MIRA

Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
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IndexError: index 39840 is out of bounds for axis 0 with size 20479 #8

Closed shaistamadad closed 2 years ago

shaistamadad commented 2 years ago

Hi,

I get an IndexError when I try to use the trained LITE model to predict gene expression for RNA data using the accessibility data. 

lite_model.fit(expr_adata=rna_sub, atac_adata=atac_sub)

IndexError: index 39840 is out of bounds for axis 0 with size 20479

Thanks so much for your help.

shaistamadad commented 2 years ago

resolved now. thank you!

AllenWLynch commented 2 years ago

Hi,

Can you provide the whole stack trace please? My intuition is that this has something to do with the TSS annotations having duplicates. Did you reannotate TSS distances using de-duplicated canonical TSS?

Thanks, AL

From: shaistamadad @.> Sent: Thursday, February 17, 2022 6:44 PM To: cistrome/MIRA @.> Cc: Subscribed @.***> Subject: [cistrome/MIRA] IndexError: index 39840 is out of bounds for axis 0 with size 20479 (Issue #8)

Hi,

I get an IndexError when I try to use the trained LITE model to predict gene expression for RNA data using the accessibility data.

lite_model.fit(expr_adata=rna_sub, atac_adata=atac_sub)

IndexError: index 39840 is out of bounds for axis 0 with size 20479

Thanks so much for your help.

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