/mnt/wigclust24/data/safe/kendall/hisat2-2.1.0/hisat2 -p 7 -5 35 --met-file /mnt/wigstore5/user/kendall/wigstore2/stillman03/hisat2_metrics.test01.txt -x /mnt/wigclust24/data/safe/kendall/hisat2-2.1.0/indexes/sc3 -1 /mnt/wigstore5/user/kendall/wigstore2/stillman03/<BARCODE_GROUP>/s_<LANE>_1_sequence.b<BARCODE>.txt.gz -2 /mnt/wigstore5/user/kendall/wigstore2/stillman03/<BARCODE_GROUP>/s_<LANE>_2_sequence.b<BARCODE>.txt.gz 2> /mnt/wigstore5/user/kendall/wigstore2/stillman03/<BARCODE_GROUP>/<SEQ_UNIT_ID>.sc3.hisat2.stderr | samtools view -Sbh - | samtools sort -o /mnt/wigstore5/user/kendall/wigstore2/stillman03/<BARCODE_GROUP>/<SEQ_UNIT_ID>.sc3.hisat2_sorted.bam - 

samtools index /mnt/wigstore5/user/kendall/wigstore2/stillman03/<BARCODE_GROUP>/<SEQ_UNIT_ID>.sc3.hisat2_sorted.bam