Sudden drop in coverage in single-cell RNA-sequencing data
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3 months ago
tien ▴ 10

Hello all, I'm working with single-cell RNA sequencing data and found some weird behavior in coverage rate. In this following picture, areas with blue circle have sharp drop in coverage number even they are not splicing site but in the middle of exon. If someone know the reason behind such behaviour?

enter image description here

Original paper of this image: https://www.researchgate.net/publication/264538496_Cell_fate_inclination_within_2-cell_and_4-cell_mouse_embryos_revealed_by_single-cell_RNA_sequencing

Thanks for your help.

singlecell • 373 views
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The circled regions essentially have no coverage, it is just some lonely reads piping up there. See the scale on the left, it's close to zero and look at the shape of the peaks, it is just rectangular blocks indicating that basically it is reads with same start and end (is that UMI scRNA-seq?) are piping up there. If not UMI can well be a PCR artifact. In contrast the lane at 2___0 has coverage, stretched out over the exon and with a complex-looking peak structure of the pileup indicating many different reads with distinct start and end positions are contributing as it should be. There is not much to interpret here other than that this exon is only expressed properly in 2___0 and basically off in the rest I think.

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In my data, they do have valid UMI so I think they are valid coverage. Any other idea about it?

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Is this screenshot your data? Are UMIs already taken care of when making the coverage plots? This question is vague and lacks details.

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Hi, sorry for my bad question. This screenshot is not about my data but my data behaves the same and I did take umi into account when plotting sashimi.

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