Recommendation for alignment visualization

pachterlab / kallistobustools

kallisto | bustools workflow for pre-processing single-cell RNA-seq data

https://kallistobus.tools/

MIT License

115 stars 29 forks source link

Recommendation for alignment visualization #47

Open jkniehaus opened 2 years ago

jkniehaus commented 2 years ago

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 commented 2 years ago

I am interested in this as well