echo use fastq-dump to download tilapia eye, embryo, brain SRA data

nohup fastq-dump --defline-seq '@$sn[_$rn]/$ri' --defline-qual '+' --outdir '/mnt/data/ncbi' --split-files SRR391705 & #embryo
nohup fastq-dump --defline-seq '@$sn[_$rn]/$ri' --defline-qual '+' --outdir '/mnt/data/ncbi' --split-files SRR391683 & #eye 1
nohup fastq-dump --defline-seq '@$sn[_$rn]/$ri' --defline-qual '+' --outdir '/mnt/data/ncbi' --split-files SRR391700 & #eye 2
nohup fastq-dump --defline-seq '@$sn[_$rn]/$ri' --defline-qual '+' --outdir '/mnt/data/ncbi' --split-files SRR391697 & #brain 1
nohup fastq-dump --defline-seq '@$sn[_$rn]/$ri' --defline-qual '+' --outdir '/mnt/data/ncbi' --split-files SRR391699 & #brain 2

echo clean up the incorrect description in fastq ID column，replace "_reverse/3" to "/2"; replace "_forward/1" to "/1"

nohup sed -i 's/\_reverse\/3/\/2/g' SRR391683_3.fastq;sed -i 's/\_reverse\/3/\/2/g' SRR391700_3.fastq;sed -i 's/\_reverse\/3/\/2/g' SRR391697_3.fastq;sed -i 's/\_reverse\/3/\/2/g' SRR391699_3.fastq > sed_edit_3.out &
nohup sed -i 's/\_forward\/1/\/1/g' SRR391683_1.fastq;sed -i 's/\_forward\/1/\/1/g' SRR391700_1.fastq;sed -i 's/\_forward\/1/\/1/g' SRR391697_1.fastq;sed -i 's/\_forward\/1/\/1/g' SRR391699_1.fastq > sed_edit_1.out &

echo Use trinity to assembling

nohup Trinity --trimmomatic --seqType fq --max_memory 38G --output '/mnt/data/ncbi/SRR391683_trinity_output' --left SRR391683_1.fastq  --right SRR391683_3.fastq --CPU 22 > Trinity_log_SRR391683.out & ;
nohup Trinity --trimmomatic --seqType fq --max_memory 38G --output '/mnt/data/ncbi/SRR391700_trinity_output' --left SRR391700_1.fastq  --right SRR391700_3.fastq --CPU 22 > Trinity_log_SRR391700.out & ;
nohup Trinity --trimmomatic --seqType fq --max_memory 38G --output '/mnt/data/ncbi/SRR391697_trinity_output' --left SRR391697_1.fastq  --right SRR391697_3.fastq --CPU 22 > Trinity_log_SRR391697.out & ;
nohup Trinity --trimmomatic --seqType fq --max_memory 38G --output '/mnt/data/ncbi/SRR391699_trinity_output' --left SRR391699_1.fastq  --right SRR391699_3.fastq --CPU 22 > Trinity_log_SRR391699.out & ;