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Recommendation for alignment visualization #47

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jkniehaus opened this issue Oct 24, 2022 · 1 comment
Open

Recommendation for alignment visualization #47

jkniehaus opened this issue Oct 24, 2022 · 1 comment

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@jkniehaus
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Hello,

I'm interested in visualizing read distribution for specific cells/clusters from scRNAseq data. Is there a method to generate a pseudoalignment bam/sam file from kb outputs to view via IGV?

I currently use kallisto quant --pseudobam ... on a subset of reads based on my cells of interest, but wasn't sure if there was a way to get this directly via kallistobustools.

Thanks!
Jesse
@gdolsten
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gdolsten commented Nov 1, 2022

I am interested in this as well

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@jkniehaus @gdolsten