/mnt/wigclust24/data/safe/kendall/hisat2-2.1.0/hisat2 -p 7 -5 35 --met-file /mnt/wigtop2/data/safe/kendall/stillman04/CHY20002.hisat2_metrics.test01.txt -x /mnt/wigclust24/data/safe/kendall/hisat2-2.1.0/indexes/sc3 -1 /mnt/wigtop2/data/safe/kendall/stillman04/b1/s_1_1_sequence.HU90.txt.gz -2 /mnt/wigtop2/data/safe/kendall/stillman04/b1/s_1_2_sequence.HU90.txt.gz 2> /mnt/wigtop2/data/safe/kendall/stillman04/b1/CHY20002.sc3.hisat2.stderr | samtools view -Sbh - | samtools sort -o /mnt/wigtop2/data/safe/kendall/stillman04/b1/CHY20002.sc3.hisat2_sorted.bam - 

samtools index /mnt/wigtop2/data/safe/kendall/stillman04/b1/CHY20002.sc3.hisat2_sorted.bam
