How to get fraction of unspliced reads for specific gene from scRNAseq Cell Ranger output

How to get fraction of unspliced reads for specific gene from scRNAseq Cell Ranger output

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Hi!

I’m new to this forum (and to bioinformatics in general), so pardon my ignorance. I looked around and couldn’t find a similar question.

I have the full Cell Ranger output (including BAM and .gtf files) for some scRNA-seq experiments and would like to get a column that represents what percentage of reads from a specific gene align to spliced vs unspliced regions for each barcode.

Is there an easy way to do this? If it’s possible in python even better, since that’s what I am mostly familiar with in terms of programming languages!

I love the forum by the way, as well as the handbook!

Thanks in advance!


scRNA-seq


python


CellRanger

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