#!/usr/bin/env sh

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

genome=../../../data/source_data/RNA_seq/seahorse/GCA_001891065.1_H_comes_QL1_v1_genomic.fna
gindex=../../../data/source_data/RNA_seq/seahorse/H_comes

#map&&assembly
mkdir ${WORKPATH}
simuoutA=$WORKPATH"/SRR3289254"
simuoutB=$WORKPATH"/SRR3289255"
mkdir $simuoutA
mkdir $simuoutB
file1="${SRCPATH}/SRR3289254_1.clean_read1.fq"
file2="${SRCPATH}/SRR3289254_2.clean_read2.fq"
file3="${SRCPATH}/SRR3289255_1.clean_read1.fq"
file4="${SRCPATH}/SRR3289255_2.clean_read2.fq"
echo assembly...
eval "./assembly_PER.sh "$file1" "$file2" "$gindex" "$simuoutA" "
eval "./assembly_PER.sh "$file3" "$file4" "$gindex" "$simuoutB" "
echo merge...
#merge
stringtie --merge $simuoutA/hisat_out.gtf $simuoutB/hisat_out.gtf > ${WORKPATH}/merged_no_G.gtf