Question: How to filter RNA editing data called by RED-ML
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gravatar for MatthewP
23 months ago by
MatthewP840
China
MatthewP840 wrote:

Hello, everyone! I use RED-ML to analyse RNA Editing events in my RNA Seq data. The result data is simple:

#P_edit: The probability of being a RNA editing site predicted by RED-ML
#Chromosome     Position        Read_depth      Reference       Reference_support_reads Alternative     
Alternative_support_reads       P_edit
chr1    14604   21      A       6       G       15      0.849387564524627
chr1    14610   21      T       5       C       16      0.516906327292332
chr1    16280   24      T       7       C       17      0.889600786631089
chr1    17606   27      A       21      G       6       0.602832411634867
chr1    19172   12      A       8       G       4       0.823503600263782
chr1    185125  6       A       2       G       4       0.752470897435155
chr1    185131  6       T       2       C       4       0.647400412860666
chr1    185428  7       A       1       G       6       0.885004885559825
chr1    186365  63      T       40      C       23      0.801998990609502
chr1    187378  22      A       9       G       13      0.785096322895598
chr1    188891  9       T       4       C       5       0.803351489912644
chr1    629218  978     A       0       G       978     0.991090135056072
chr1    631193  44      A       4       G       40      0.94447283158624
chr1    632346  339     T       0       C       339     0.845537964553492
chr1    633630  10      T       1       C       9       0.605907924765477
chr1    633714  16      A       2       G       14      0.539893855272783
chr1    634112  1211    T       4       C       1207    0.803272961009867

However I don't have experience at filtering such data. Shall I filter by comparing with data from RNA Editing database(DARNED and RADAR)? Do I need to consider read deapth between Reference and Alternate? P_edit >= 0.9? Tell me your experience thanks!

rna-seq rna editing • 404 views
ADD COMMENTlink written 23 months ago by MatthewP840
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