Total sequence with eccessive missing nucleotides

[Xiezhouwei2024]

When I run redinet using the result file of reditools2, the following report will appear：
My redinet code：

python3 /data/work/REDInet_all/REDInet/Package/Utilities/REDInet_Inference.py \
--I /data/work/REDInet_all/REDInet/Data/ \
--O /data/work/REDInet_all/REDInet/Data/ \
--A GRCh38 \
--C 2 \
--M 2 \
--S 30 \
--R yes \
--N T21E6_chr2.txt.gz

Final Report:
Inference on T21E6_chr2.txt start.
Inference on T21E6_chr2.txt end. Elapsed time 0:00:05.654936.
[2025-11-24 14:29:49.977580] T21E6_chr2.txt processing start.
Total evaluated rows in T21E6_chr2.txt: 118220947
Total discarded sites in T21E6_chr2.txt: 14624.
Total candidates sites in T21E6_chr2.txt: 297968.
Candidates sites identification in T21E6_chr2.txt end. Elapsed time: 0:03:30.421747.
**Total sequence with eccessive missing nucleotides in T21E6_chr2.txt: 296167.**
Total extracted sites in T21E6_chr2.txt: 1801.
Features extraction in T21E6_chr2.txt end. Elapsed time 0:25:39.762869

The biggest problem is excessive nucleotide deletions. Is this normal? Do I have any solution?
I have tried adjusting the parameters S and R, but the results have not improved.

In addition, the code of reditools2 is attached (I think the requirement is that the filtering conditions are as loose as possible, I think mine is already very loose)

#Reditools2
python3 /data/work/Reditools2_all/reditools2.0-master/src/cineca/reditools.py \
-f /data/users/liyuejiao/online/project/t21/rna_editing/dnbc4tools/T21E6_Midbrain/T21E6_Midbrain/outs/anno_decon_sorted.bam \
-r /data/input/Files/chenjin/W202504210003221/reference/WGS_hg38.fa \
-o /data/work/Reditools2_all/Reditools2_result/T21E6_chr1.txt \
-l 1 -q 25 -bq 25 -men 5 -C -g chr1