I'm running rmats/4.1.2 to detect the splicing events.

python /software/rmats/4.1.2/rmats.py --gtf  /reference_annotation/Homo_sapiens.GRCh38.86.gtf -t paired \
--b1 ko_1.txt --b2  wt_1.txt --od /Rmats_test \
--tmp /Rmats_test --libType fr-secondstrand --readLength 63 \
--nthread 4 --tstat 4 --variable-read-length --novelSS --allow-clipping

From the outcome file

USED: 49050150
NOT_PAIRED: 0
NOT_NH_1: 0
NOT_EXPECTED_CIGAR: 3190321
NOT_EXPECTED_READ_LENGTH: 0
NOT_EXPECTED_STRAND: 0
EXON_NOT_MATCHED_TO_ANNOTATION: 354260651
JUNCTION_NOT_MATCHED_TO_ANNOTATION: 53086428
CLIPPED: 0
TOTAL_FOR_BAM: 459587550
WT_1out.bam

Same report for the other file also. I have huge number of NOT MATCHED alignment between my BAM and GTF. I checked they are the same GFT file. Is there any other reason? Second one is NOT_PAIRED: 0 I did samtools stat

SN  reads mapped and paired:    459587550   # paired-end technology bit set + both mates mapped
SN  reads properly paired:  459587550   # proper-pair bit set
SN  reads paired:   459587550   # paired-end technology bit set
SN  inward oriented pairs:  229735745
SN  outward oriented pairs: 58030
SN  pairs with other orientation:   0
SN  pairs on different chromosomes: 0
SN  percentage of properly paired reads (%):    100.0

So i'm confused now. is there any qc i can do? any suggestion?

Thanks