STAR \
    --genomeDir star \
    --readFilesIn input1/RAP1_UNINDUCED_REP1_primary.fastq.gz  \
    --runThreadN 4 \
    --outFileNamePrefix RAP1_UNINDUCED_REP1. \
    --sjdbGTFfile genome_gfp.gtf \
    --quantMode TranscriptomeSAM --outSAMtype BAM Unsorted --outSAMattributes NH HI AS NM MD --readFilesCommand zcat --twopassMode Basic --runRNGseed 0 --outFilterMultimapNmax 20 --alignSJDBoverhangMin 1 --outSAMstrandField intronMotif --quantTranscriptomeSAMoutput BanSingleEnd --outSAMattrRGline 'ID:RAP1_UNINDUCED_REP1' 'SM:RAP1_UNINDUCED_REP1'
	

if [ -f RAP1_UNINDUCED_REP1.Unmapped.out.mate1 ]; then
    mv RAP1_UNINDUCED_REP1.Unmapped.out.mate1 RAP1_UNINDUCED_REP1.unmapped_1.fastq
    gzip RAP1_UNINDUCED_REP1.unmapped_1.fastq
fi
if [ -f RAP1_UNINDUCED_REP1.Unmapped.out.mate2 ]; then
    mv RAP1_UNINDUCED_REP1.Unmapped.out.mate2 RAP1_UNINDUCED_REP1.unmapped_2.fastq
    gzip RAP1_UNINDUCED_REP1.unmapped_2.fastq
fi