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

…

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/bash

genome=$1
index=${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 $index

hisat2 -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}.sam


samtools sort -@ 20 \
                  -o ${index}.sorted.bam \
                      -O BAM \
                ${index}.sam

PSSA_align

#!/bin/bash

export 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