Hi!

I am using the STAR aligner to align my RNA-seq data to hg38, and my outputs are all inverted when I visualize them in the IGV (they all go to the opposite direction to the gene)

RNA-seq library prep was performed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina

I am using the following parameters:

STAR --runThreadN 12 \ 
--genomeDir /lcrb/Alumni/Ofri/genome_directory \ 
--readFilesCommand zcat \
--readFilesIn ${name}.fastq.gz \
--quantMode GeneCounts\
--outSAMtype BAM SortedByCoordinate --outFileNamePrefix ../STAR_OUT_readStrand/${name} ; done

Any leads for why do I see al my reads inverted?

Thanks!!