跟着Nature Communications学习Hisat-Trinity-PASA等分析流程

一边学习，一边总结，一边分享！

详细教程请访问：
组学分析流程

本期分析流程

1. Hisat2-Samtools
2. Trinity_GG_denovo
3. PASA

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本期教程文章

题目：Genomic insights into local adaptation and future climate-induced vulnerability of a keystone forest tree in East Asia

Hisat2-samtools分析流程

#!/bin/bashgenome=$1
index=${genome%.*}
rna_1_fq=`cat $2|grep 1P|sed ":a;N;s/\n/,/g;ta"` #1.fq path list
rna_2_fq=`cat $2|grep 2P|sed ":a;N;s/\n/,/g;ta"` #2.fq path list#echo $index
hisat2-build -p 20 $genome $indexhisat2 -x $index \-1 $rna_1_fq\-2 $rna_2_fq\--threads 20 \--min-intronlen 20 \--max-intronlen 20000 \--dta \--score-min L,0.0,-0.4 \-S ${index}.samsamtools sort -@ 20 \-o ${index}.sorted.bam \-O BAM \${index}.sam

PSSA_align

#!/bin/bashexport PATH="$PATH:/usr_storage/jcf/.conda/envs/PASA"
source  /pub_storage2/new_PASA/.bashrc#cat $Trinity_GG $Trinity_denovo >transcripts.fasta #
transcripts_fasta="$1" # transcripts.fasta generated from merging fasta file of Trinity denovo and Trinity genome guided mo