Re: Looking fo help for the usage of DaPars

[Xia, Zheng]

Hi Yong,

     Could you show me the output file of your result? 

Thanks,

Zheng

On Jul 8, 2015, at 8:12 AM, Zeng, Yong <YZ...@cvm.tamu.edu> wrote:

Dear Dr. Zheng Xia

 

I am writing to look for help for the usage of DaPars. As the your paper said DaPars can predict de novo distal poly(A) sites directly from RNA-seq, however, they were not included in the output results. How can I get the location of the estimate distal poly(A) site through the DaPars?

 

Thanks a lot in advance for your help  and looking forward your reply.

 

Best regards

Yong

 

Department of Veterinary Integrative Biosciences

Texas A&M University

[zxue....@gmail.com]

Hi Zheng,

I have exactly the same question, my output look like

Gene fit_value Predicted_Proximal_APA Loci A_1_long_exp A_1_short_exp A_1_PDUI B_1_long_exp B_1_short_exp B_1_PDUI Group_A_Mean_PDUI Group_B_Mean_PDUI PDUI_Group_diff P_val adjusted.P_val Pass_Filter
0 NM_001904|CTNNB1|chr3|+ 232572.8 41281399 chr3:41280625-41281939 205.86 828.36 0.20 221.07 994.66 0.18 0.20 0.18 0.02 0.331265 0.516548 N
8 NM_001098209|CTNNB1|chr3|+ 40101.2 41281397 chr3:41281151-41281939 256.85 1001.77 0.20 263.88 1270.85 0.17 0.20 0.17 0.03 0.031483 0.061626 N
86 NM_001098210|CTNNB1|chr3|+ 191454.4 41281511 chr3:41281310-41281939 289.93 465.07 0.38 318.83 532.64 0.37 0.38 0.37 0.01 0.718251 0.892960 N

So where is the predicted distal cleavage site, please? Is the Loci column from annotation? I used the hg19_refseq_extracted_3UTR.bed file packaged inside the DaPars https://github.com/ZhengXia/dapars.


Thanks!
Zhuyi