High % of unspliced from 10X scRNAseq in tissues

[denvercal1234GitHub]

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]

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]

Dear all,

Do you guys have solved this issue? Any ideas?

Thanks Yayan

[LikaiTan]

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]

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

[karlie002]

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"