Alignment
blast
Mapping
BWT算法
HISAT2 summary stats: Total pairs: 32617089 Aligned concordantly or discordantly 0 time: 8741165 (26.80%) Aligned concordantly 1 time: 21568529 (66.13%) Aligned concordantly >1 times: 1367753 (4.19%) Aligned discordantly 1 time: 939642 (2.88%) Total unpaired reads: 17482330 Aligned 0 time: 10036571 (57.41%) Aligned 1 time: 6761396 (38.68%) Aligned >1 times: 684363 (3.91%) Overall alignment rate: 84.61% fastp: reads passed filters: 65.234178 M (97.655265%) 32617089*2=65234178
#!/bin/bash if [ "$#" -ne 1 ]; then echo -e "Incorrect number of parameters! Usage:\n index-gtf.sh <file.gtf(.gz)>" >&2 exit 1 fi gtf="$1" if [[ $gtf =~ \.gz$ ]]; then output=${gtf%.gtf.gz}.sorted.gtf.gz zcat $gtf | awk '!( $0 ~ /^#/ )' | sort --parallel=4 -S4G -k1,1 -k4,4n | bgzip -c > $output else output=${gtf%.gtf}.sorted.gtf.gz cat $gtf | awk '!( $0 ~ /^#/ )' | sort --parallel=4 -S4G -k1,1 -k4,4n | bgzip -c > $output fi tabix $output cat Rattus_norvegicus.Rnor_6.0.104.gtf | awk '!( $0 ~ /^#/ )' | sort --parallel=4 -S4G -k1,1 -k4,4n | > Rattus_norvegicus.Rnor_6.0.104.sorted.gtf bgzip Rattus_norvegicus.Rnor_6.0.104.sorted.gtf tabix Rattus_norvegicus.Rnor_6.0.104.sorted.gtf