Junction annotation question (unknown_strand)

[SaraAlidadiani]

Hi,

I was using regtools junction annotation to annotate a junction bed file of junction extract output. In my results, I see a lot of significant events that are classified as unknown_strand. The junction file was extracted from STAR aligned BAM file, and I used GENCODE v42 .
As it was from Standard Illumina and unstranded, I used -s XS.

The code I used is:

for bamfile in `ls /home/leafcutter-bam/*.bam`; do
    echo Converting $bamfile to $bamfile.junc
    samtools index $bamfile
    regtools junctions extract -a 8 -m 50 -M 500000 $bamfile -o $bamfile.junc -s XS
    echo $bamfile.junc >> test_juncfiles_mayo.txt
done

Why are these events categorized as "unkown_strand"?
Could you help me with this, please?