/mnt/wigclust24/data/safe/kendall/hisat2-2.1.0/hisat2 -p 1 -5 0 --met-file /mnt/wigtop2/data/safe/kendall/stillman05/<SEQ_UNIT_ID>.hisat2_metrics.test01.txt -x /mnt/wigclust24/data/safe/kendall/hisat2-2.1.0/indexes/sc3 -1 /mnt/wigtop2/data/safe/kendall/stillman05/<SSDP>/s_<LANE>_1_sequence.<SAMPLE_NUMBER>.txt.gz -2 /mnt/wigtop2/data/safe/kendall/stillman05/<SSDP>/s_<LANE>_2_sequence.<SAMPLE_NUMBER>.txt.gz 2> /mnt/wigtop2/data/safe/kendall/stillman05/<SSDP>/<SEQ_UNIT_ID>.sc3.hisat2.stderr | samtools view -Sbh - | samtools sort -o /mnt/wigtop2/data/safe/kendall/stillman05/<SSDP>/<SEQ_UNIT_ID>.sc3.hisat2_sorted.bam - 

samtools index /mnt/wigtop2/data/safe/kendall/stillman05/<SSDP>/<SEQ_UNIT_ID>.sc3.hisat2_sorted.bam