--runMode alignReads \
--alignIntronMax 10000 \
--alignMatesGapMax 11000 \
--alignSJDBoverhangMin 1 \
--alignSJoverhangMin 10 \
--outSJfilterOverhangMin -1 15 15 15 \
--outSJfilterCountTotalMin -1 2 2 2 \
--outSJfilterCountUniqueMin -1 2 2 2 \
--outFilterType BySJout \
--outFilterMismatchNmax 2 \
--outFilterMismatchNoverLmax .05 \
--twopassMode Basic \
--genomeDir $genome_index_dir \
--limitBAMsortRAM "$RAM"000000000 \
--outFilterIntronMotifs RemoveNoncanonicalUnannotated \
--outReadsUnmapped Fastx \
--outFilterMultimapNmax 100 \
--outSAMmultNmax 100 \
--outSAMattributes NH HI AS nM NM MD jM jI XS \
--outSAMprimaryFlag AllBestScore \
--outSAMtype BAM Unsorted \
--outTmpDir $temp_dir_s \
--quantMode GeneCounts \
--runRNGseed 12345 \
--runThreadN $CPUS \
--sjdbGTFfile $annotation_gff
