A question about align reverse forward stranded RNAseq data

[QianhuiWan]

Hello, I have an issue where the Watson BAM file is much larger than the Crick BAM file after using STAR for alignment for reverse forward stranded RNAseq data. This issue did not appear when using HISAT2 for alignment. I haven’t been able to figure out the main reason for this problem. Could you please help me understand this issue? Thank you so much!

Below is the code I have used:
${STAR} --genomeDir /hg38_p14/STAR_hg38_p14 \ --readFilesIn ${outdir}/${sample_name}_R1_trimmed.fastq.gz ${outdir}/${sample_name}_R2_trimmed.fastq.gz \ --readFilesCommand zcat \ --outFilterMultimapNmax 100 --winAnchorMultimapNmax 100 \ --outSAMtype BAM SortedByCoordinate \ --outFileNamePrefix ${outdir}/${sample_name}_ \ --runThreadN 8

Best regards
Qianhui