2020-07-24

zhiwufy@DESKTOP-TC540TA:/mnt/e/dai$ hisat2 -f -x mixgenome  -p 24 -U all.fasta -S all-picea.sam
70 reads; of these:
  70 (100.00%) were unpaired; of these:
    11 (15.71%) aligned 0 times
    44 (62.86%) aligned exactly 1 time
    15 (21.43%) aligned >1 times
84.29% overall alignment rate
zhiwufy@DESKTOP-TC540TA:/mnt/e/dai$ samtools view -bS  all-picea.sam  >all-picea.bam
zhiwufy@DESKTOP-TC540TA:/mnt/e/dai$ samtools sort all-picea.bam  -o all-picea.sort.bam
zhiwufy@DESKTOP-TC540TA:/mnt/e/dai$ samtools index  all-picea.sort.bam
zhiwufy@DESKTOP-TC540TA:/mnt/e/dai$ stringtie all-picea.sort.bam -o all-picea.sort.bam.gtf
zhiwufy@DESKTOP-TC540TA:/mnt/e/dai$ stringtie all-picea.sort.bam -o all-picea.sort.bam.gff3