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velocyto-team / velocyto.py

RNA velocity estimation in Python
http://velocyto.org/velocyto.py/
BSD 2-Clause "Simplified" License
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High % of unspliced from 10X scRNAseq in tissues #364

Open denvercal1234GitHub opened 1 year ago

denvercal1234GitHub commented 1 year ago

Hi there,

Thanks for the package.

I obtained a very high % of unspliced reads (65%) in the samples of human tonsils.

Do you know if this high % is technical error of the sample or the way I run velocyto?

velocyto run10x -m ....../Velocyto/mm10_rmsk.gtf ....../count_R1 ......./Velocyto/gencode.v32.primary_assembly.annotation.gtf

Thanks for your help

Related #342

LikaiTan commented 1 year ago

I have the same issue. My samples were human tissue, the datasets were generated by 10x 5'RNA seq. I analyzed the data via run10x and dropest, and I got the same result.

YayanFeng55 commented 1 year ago

Dear all,

Do you guys have solved this issue? Any ideas?

Thanks Yayan

LikaiTan commented 1 year ago

In my case, not at all....On 9 Aug 2023 00:18, YayanFeng55 @.***> wrote: Dear all, Do you guys have solved this issue? Any ideas? Thanks Yayan

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you commented.Message ID: @.***>

mbrochut commented 8 months ago

I do have the same problem. Does anybody have solved the problem?

karlie002 commented 5 months ago

I have met the same problem , high percentage of unspliced reads in one subset of all my samples, while it's ok if group by "orig.ident"