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YiPeng-Gao / scDaPars

Dynamic Analysis of Alternative Polyadenylation from single-cell RNA-seq (scDaPars)
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What does NA represent in the original PDUI matrix？ #16

Open AIBio opened 2 years ago

AIBio commented 2 years ago

Hi, I noticed that there are a lot of 'NA' values in raw PDUI matrix generated from DaPars2. Does these ’NA‘ values mean that it is uncertain whether to use a distal polyA site for a certain gene? Could you explain the specific meaning about 'NA' values? Note: My data is scRNAseq data generated with SMART-seq2 protocol. Thanks Hanwen Yu 2021/07/18

yangfeizZZ commented 2 years ago

would you telling me your E-mail or QQ number？I do it now. we can communicate each other .

YiPeng-Gao commented 2 years ago

Hi, I noticed that there are a lot of 'NA' values in raw PDUI matrix generated from DaPars2. Does these ’NA‘ values mean that it is uncertain whether to use a distal polyA site for a certain gene? Could you explain the specific meaning about 'NA' values? Note: My data is scRNAseq data generated with SMART-seq2 protocol. Thanks Hanwen Yu 2021/07/18

NA means that gene does not enough coverage to be calculated. You can adjust your cutoff in the DaPars configure file.

AIBio commented 2 years ago

would you telling me your E-mail or QQ number？I do it now. we can communicate each other .

my QQ: 1096123550

AIBio commented 2 years ago

Hi, I noticed that there are a lot of 'NA' values in raw PDUI matrix generated from DaPars2. Does these ’NA‘ values mean that it is uncertain whether to use a distal polyA site for a certain gene? Could you explain the specific meaning about 'NA' values? Note: My data is scRNAseq data generated with SMART-seq2 protocol. Thanks Hanwen Yu 2021/07/18

NA means that gene does not enough coverage to be calculated. You can adjust your cutoff in the DaPars configure file.

Thank you~~~

YiPeng-Gao commented 2 years ago

NA means the coverage is not enough for DaPars2 to calculate the initial PDUI values, so it needs to be Imputed.

Yipeng Gao Ph.D. candidate - Quantitative & Computational Biosciences Laboratory of Chris Amos, Ph.D. Institute for Clinical and Translational Research Baylor College of Medicine

On Sep 30, 2021, at 02:55, Hanwen_Yu @.***> wrote:

Hi, I noticed that there are a lot of 'NA' values in raw PDUI matrix generated from DaPars2. Does these ’NA‘ values mean that it is uncertain whether to use a distal polyA site for a certain gene? Could you explain the specific meaning about 'NA' values? Note: My data is scRNAseq data generated with SMART-seq2 protocol. Thanks Hanwen Yu 2021/07/18

NA means that gene does not enough coverage to be calculated. You can adjust your cutoff in the DaPars configure file.

Thank you~~~

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