Difference in sashimi plot between single-cell versus bulk RNA-seq data

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2.3 years ago

tien ▴ 40

Hello, I'm using pysashimi to draw splicing junction plot for both single-cell and bulk RNA data but I observe that the coverage rate in bulk data (green) is more likely to spread over position than single-cell data (red). I know that they are from different sample, different gene but to me, it seems to be due to sequencing techique or the way they calculate coverage. If anyone understand this situation?

Thanks for any help.

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pysashimi • 887 views

ADD COMMENT • link 2.3 years ago by tien ▴ 40

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I think this is referring to fact that single cell data is going to be 3' focused where as bulk spread over the length of the gene body because of the way the two technologies work.

ADD REPLY • link 2.3 years ago by GenoMax 147k

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Unless they are doing Smart-Seq which is full-length? Also splicing will be exon-centric... so they are saying the bulk reads are bleeding into the introns (i assume).