比對到miRNA base

下載 ：hairpin.fa，?mature.fa??http://www.mirbase.org/ftp.shtml??hairpin.fa?

提取?Brassica.fa??miRNA

nohup perl -alne '{if(/^>/){if(/Brassica rapa/){$tmp=1}else{$tmp=0}};next if $tmp!=1;s/U/T/g if !/>/;print }' hairpin.fa > hairpin.Bra.fa

perl -alne '{if(/^>/){if(/Brassica oleracea/){$tmp=1}else{$tmp=0}};next if $tmp!=1;s/U/T/g if !/>/;print } ' hairpin.fa >hairpin.Bol.fa

perl -alne '{if(/^>/){if(/Brassica napus/){$tmp=1}else{$tmp=0}};next if $tmp!=1;s/U/T/g if !/>/;print }' hairpin.fa >hairpin.Bna.fa

比對到 （-f 是指輸入fa 序列）

nohup ls *.fa | while read id; do bowtie2 -f -x /baicai2/weiyx/smallRNA/miRNA/bowtie2_index/hairpin_bra -U $id -S ${id%%.*}.hairpin.sam; done &

好，這一步完成。