Understanding/filtering RRD jacusa2 output

[CelineLabbeCurie]

Hello,

I'm comparing two RNA samples (RRD - RNA RNA differences).
As Michael Piechotta advised, I've filtered all SNPs on the output of Jacusa2 with bedtools.

Here is an example of what I have :

#contig     start end   name  score strand      bases11     bases12     bases21     bases22     info  filter      ref
chr1  1223838     1223839     chr1:1223838-1223839:-  3.816651429035119 -     C->T  C->T  0,2629,0,17 0,2050,0,8  0,2087,0,0  0,2195,0,3  *     *     C
chr1  1254929     1254930     chr1:1254929-1254930:-  7.649157863077676 -     C->T  C->T  0,904,0,20  0,696,0,19  0,678,0,5   0,602,0,1   *     *     C
chr1  1255001     1255002     chr1:1255001-1255002:-  2.6378000453478307      -     C->T  C->T  0,1122,0,9  0,781,0,5   0,805,0,1   0,738,0,0   *     *     C
chr1  1255185     1255186     chr1:1255185-1255186:-  5.54518504718726  -     C->T  C->T  0,1393,0,13 0,1103,0,13 0,976,0,2   0,1026,0,0  *     *     C

So I understand that the score indicates a difference between the two conditions. Here, it seems to me that bases11/bases12 are more edited than bases21/bases22 .
When the score is calculated, it indicates a difference but do we know which condition is different (as in more edited) from the other or just that there is a difference between the two ?
I'd like to select the lines where cond2 is more edited than cond1. Is there a way to do that ? Can I rely only on the score ? Do I have to comme back to the bases11/12/21/22 column to know wich condition is more edited ?

I've already applied some filters :

Coverage >= 2
Remove sites with more than 2 observed bases
Retain only robust sites (dplyr::filter(robust(bases)))
Remove Artefacts (D option of JACUSA)

What I'd like, is to have a list of sites (positions, strand, score...) differentially edited in my test condition as in more C>T editing in cond2 than in cond1. Could you please guide me ?

Also, how can I determine a good threshold for the score ?

And, just to be sure. My command line was like :
java -jar $JACUSA2 call-2 -a D -p 8 -P RF-FIRSTSTRAND -r Jacusa2_output.out cond1_rep1_Aligned_filtered_sorted_MD.bam,cond1_rep2_Aligned_filtered_sorted_MD.bam cond2_rep1_Aligned_filtered_sorted_MD.bam,cond2_rep2_Aligned_filtered_sorted_MD.bam

So the columns "bases11 bases21 bases 21 bases22 of my output will be in that order : cond1_rep1 cond1_rep2 cond2_rep1 cond2_rep2 ? Is that correct please ?

Last question, I see there is an option -B READ-TAG. I'm not sure I understand correctly. Can I use that option to have only C>T substition in my output ?

I'm a little lost... I'd appreciate any help :)
Thanks a lot !
Best,

[Chan-W00]

Did you catch it? I'm confused about what you asked before.