#!/usr/bin/env sh

SRCPATH="../../../data/source_data/RNA_seq/rainbow_trout"
WORKPATH="../../../data/processing_data/Real_data/rainbow_trout"

genome=../../../data/source_data/RNA_seq/rainbow_trout/CCAF010000001-CCAF010192415.fasta
gindex=../../../data/source_data/RNA_seq/rainbow_trout/rt

#map&&assembly
mkdir ${WORKPATH}
simuoutA=$WORKPATH"/SRR1104583"
simuoutB=$WORKPATH"/SRR1104584"
simuoutC=$WORKPATH"/SRR1104585"
mkdir $simuoutA
mkdir $simuoutB
mkdir $simuoutC
file1="${SRCPATH}/SRR1104583_1.clean_read1.fq"
file2="${SRCPATH}/SRR1104584_1.clean_read1.fq"
file3="${SRCPATH}/SRR1104585_1.clean_read1.fq"
echo assembly...
eval "./assembly_SER.sh "$file1" "$gindex" "$simuoutA" "
eval "./assembly_SER.sh "$file2" "$gindex" "$simuoutB" "
eval "./assembly_SER.sh "$file3" "$gindex" "$simuoutC" "
echo merge...
#merge
stringtie --merge $simuoutA/hisat_out.gtf $simuoutB/hisat_out.gtf $simuoutC/hisat_out.gtf > ${WORKPATH}/merged_no_G.gtf