cd /home/iwasaki

mkdir Zhang

cd /home/iwasaki/Zhang

mkdir RawFastq

scp -i ~/.ssh/riboseq_iwasaki /Users/garapa5/Dropbox/Mac/Documents/Profiling/220303_Co_transriptome_assembly/Analysis/220303/list.txt iwasaki@172.18.88.45:/home/iwasaki/Zhang/RawFastq
scp -i ~/.ssh/riboseq_iwasaki /Users/garapa5/Dropbox/Mac/Documents/Profiling/220303_Co_transriptome_assembly/Analysis/220303/fastq-dump.sh iwasaki@172.18.88.45:/home/iwasaki/Zhang/RawFastq

cd /home/iwasaki/Zhang/RawFastq

vdb-config --interactive
#x For exit

nohup bash fastq-dump.sh &


##########Merge the reads
cat SRR11887729.fastq.gz SRR11887726.fastq.gz SRR11887740.fastq.gz > Conidia.fastq.gz &
cat SRR11887739.fastq.gz SRR11887738.fastq.gz SRR11887737.fastq.gz > Mycelia.fastq.gz &



##########Removing adaptor sequences from library
nohup fastp -i /home/iwasaki/Zhang/RawFastq/Conidia.fastq.gz -o /home/iwasaki/Zhang/RawFastq/Conidia_clipped.fastq -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --length_limit 149 -w 12 -h /home/iwasaki/Zhang/RawFastq/Conidia_clipped_clipped.html &
nohup fastp -i /home/iwasaki/Zhang/RawFastq/Mycelia.fastq.gz -o /home/iwasaki/Zhang/RawFastq/Mycelia_clipped.fastq -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --length_limit 149 -w 12 -h /home/iwasaki/Zhang/RawFastq/Mycelia_clipped_clipped.html &




##########mapping by star
cd /home/iwasaki/Zhang

mkdir Alignment

cd /home/iwasaki/Zhang/Alignment


nohup STAR --genomeDir /home/genome/Colletotrichum_orbiculare/GCA_000350065.2/C.orbiculare_knownGene_STAR --readFilesIn /home/iwasaki/Zhang/RawFastq/Conidia_clipped.fastq --runThreadN 6 --outSAMtype BAM SortedByCoordinate --outFileNamePrefix /home/iwasaki/Zhang/Alignment/Conidia --limitBAMsortRAM 10000000000 &

nohup STAR --genomeDir /home/genome/Colletotrichum_orbiculare/GCA_000350065.2/C.orbiculare_knownGene_STAR --readFilesIn /home/iwasaki/Zhang/RawFastq/Mycelia_clipped.fastq --runThreadN 6 --outSAMtype BAM SortedByCoordinate --outFileNamePrefix /home/iwasaki/Zhang/Alignment/Mycelia --limitBAMsortRAM 10000000000 &


stringtie -G /home/genome/Colletotrichum_orbiculare/GCA_000350065.2/genomic.gff -l Conidia -o Conidia.gtf ConidiaAligned.sortedByCoord.out.bam &

stringtie -G /home/genome/Colletotrichum_orbiculare/GCA_000350065.2/genomic.gff -l Mycelia -o Mycelia.gtf MyceliaAligned.sortedByCoord.out.bam &

######

gffread  Conidia.gtf -g /home/genome/Colletotrichum_orbiculare/GCA_000350065.2/GCA_000350065.2_KSG_Corb_v2_genomic.fna -E -o  Conidia.gff3

gffread  Mycelia.gtf -g /home/genome/Colletotrichum_orbiculare/GCA_000350065.2/GCA_000350065.2_KSG_Corb_v2_genomic.fna -E -o  Mycelia.gff3
######

grep reference_id Conidia.gtf | awk -F'\t' '{if($3 == "transcript"){print $0}}' OFS='\t' | awk -F'\t' '{print $9}' OFS='\t'| awk -F';' '{print $1, $3}' OFS='\t' | sed -e 's/"//g' | sed -e 's/gene_id //' | sed -e 's/ reference_id rna-gnl|WGS:AMCV|//' > Conidia_id.txt
 
awk -F'\t' '{if($3 == "transcript"){print $0}}' OFS='\t' Conidia.gtf | awk -F'\t' '{print $7, $9}' OFS='\t' | awk -F';' '{print $1, $2}' OFS='\t' | awk -F'\t' '{print $1, $3}' OFS='\t'|sed -e 's/"//g' | sed -e 's/ transcript_id //' > Conidia_id_full.txt


#run R script 220311.R to make Conidia_5UTR.gtf and Conidia_5UTR.gff3


gffread  Conidia_5UTR.gff3 -g /home/genome/Colletotrichum_orbiculare/GCA_000350065.2/GCA_000350065.2_KSG_Corb_v2_genomic.fna -E -w Conidia_5UTR.fasta​&

######

grep reference_id Mycelia.gtf | awk -F'\t' '{if($3 == "transcript"){print $0}}' OFS='\t' | awk -F'\t' '{print $9}' OFS='\t'| awk -F';' '{print $1, $3}' OFS='\t' | sed -e 's/"//g' | sed -e 's/gene_id //' | sed -e 's/ reference_id rna-gnl|WGS:AMCV|//' > Mycelia_id.txt

awk -F'\t' '{if($3 == "transcript"){print $0}}' OFS='\t' Mycelia.gtf | awk -F'\t' '{print $7, $9}' OFS='\t' | awk -F';' '{print $1, $2}' OFS='\t' | awk -F'\t' '{print $1, $3}' OFS='\t'|sed -e 's/"//g' | sed -e 's/ transcript_id //' > Mycelia_id_full.txt


#run R script 220313.R to make Mycelia_5UTR.gtf and Mycelia_5UTR.gff3

gffread  Mycelia_5UTR.gff3 -g /home/genome/Colletotrichum_orbiculare/GCA_000350065.2/GCA_000350065.2_KSG_Corb_v2_genomic.fna -E -w Mycelia_5UTR.fasta​&




#Conidia ID list
/home/iwasaki/Zhang/Alignment/Conidia_id_full_1.txt

#Conidia 5UTR fasta
/home/iwasaki/Zhang/Alignment/Conidia_5UTR.fasta

#Mycelia ID list
/home/iwasaki/Zhang/Alignment/Mycelia_id_full_1.txt


#Mycelia 5UTR fasta
/home/iwasaki/Zhang/Alignment/Mycelia_5UTR.fasta

