# MPE

##mapping reads back to evigene .tr output using STAR to check the percentage of reads that map

# STAR --version
## STAR_2.6.1d
#
# samtools --version
## samtools 1.9-52-g651bf14
## Using htslib 1.9-90-ga80f5fd
## Copyright (C) 2019 Genome Research Ltd.


#ulimit default 1024
ulimit -n 10000

#############
###Desiree###
#############

mkdir ../input/Desiree_star-index

# generate mapping reference index for merged okay and alt evigene transcripts
STAR --runThreadN 32 --runMode genomeGenerate --genomeDir ../input/Desiree_star-index \
--genomeFastaFiles ../../_A_01_evigene/output/Desiree.tr.fasta --limitGenomeGenerateRAM=242371378560

## mapping only Illumina reads!
#you cannot have paired and single end reads in same mapping!!!

#Desiree STAR SE mapping
STAR \
--runMode alignReads \
--runThreadN 32 \
--genomeDir ../input/Desiree_star-index \
--readFilesIn \
../../../_S_01_sequences/output/Desiree_cleaned_Illumina_SE.fastq \
--outFileNamePrefix ../output/Desiree_mapToEvigene_STAR_SE_ \
--outSAMtype BAM SortedByCoordinate


../../../_S_01_sequences/output/Desiree_cleaned_Illumina_PE.fastq \
 out1=../input/Desiree_cleaned_Illumina_PE_R1.fastq out2=../input/Desiree_cleaned_Illumina_PE_R2.fastq \
 fastawrap=700 overwrite=true ignorebadquality=t int=t


#Desiree STAR PE mapping
STAR \
--runMode alignReads \
--runThreadN 32 \
--genomeDir ../input/Desiree_star-index \
--readFilesIn \
../input/Desiree_cleaned_Illumina_PE_R1.fastq \
../input/Desiree_cleaned_Illumina_PE_R2.fastq \
--outFileNamePrefix ../output/Desiree_mapToEvigene_STAR_PE_ \
--outSAMtype BAM SortedByCoordinate




###########
###PW363###
###########

mkdir ../input/PW363_star-index

# generate mapping reference index for merged okay and alt evigene transcripts
STAR --runThreadN 32 --runMode genomeGenerate --genomeDir ../input/PW363_star-index \
--genomeFastaFiles ../../_A_01_evigene/output/PW363.tr.fasta --limitGenomeGenerateRAM=242371378560

## mapping only Illumina reads!
#you cannot have paired and single end reads in same mapping!!!


../../../_S_01_sequences/output/PW363IlluminaDSNPE90.fastq.gz \
out1=../input/PW363_cleaned_Illumina_PE_R1.fastq \
out2=../input/PW363_cleaned_Illumina_PE_R2.fastq \
fastawrap=700 overwrite=true int=t

#PW363 STAR PE mapping
STAR \
--runMode alignReads \
--runThreadN 32 \
--genomeDir ../input/PW363_star-index \
--readFilesIn \
../input/PW363_cleaned_Illumina_PE_R1.fastq \
../input/PW363_cleaned_Illumina_PE_R2.fastq \
--outFileNamePrefix ../output/PW363_mapToEvigene_STAR_PE_ \
--outSAMtype BAM SortedByCoordinate




###########
###Rywal###
###########

mkdir ../input/Rywal_star-index

# generate mapping reference index for merged okay and alt evigene transcripts
STAR --runThreadN 32 --runMode genomeGenerate --genomeDir ../input/Rywal_star-index \
--genomeFastaFiles ../../_A_01_evigene/output/Rywal.tr.fasta --limitGenomeGenerateRAM=242371378560

## mapping only Illumina reads!
#you cannot have paired and single end reads in same mapping!!!

gunzip /DATB/fitows_prenos/markop/potato_transcriptome_assemblies/Rywal/0_cleaned_reads/RywalNahG_cleaned_Illumina_SE.fastq.gz

#Rywal STAR SE mapping
STAR \
--runMode alignReads \
--runThreadN 32 \
--genomeDir ../input/Rywal_star-index \
--readFilesIn \
../../../_S_01_sequences/output/RywalNahG_cleaned_Illumina_SE.fastq \
--outFileNamePrefix ../output/Rywal_mapToEvigene_STAR_SE_ \
--outSAMtype BAM SortedByCoordinate


../../../_S_01_sequences/output/RywalNahG_cleaned_Illumina_PE.fastq.gz \
 out1=../input/Rywal_cleaned_Illumina_PE_R1.fastq out2=../input/Rywal_cleaned_Illumina_PE_R2.fastq \
 fastawrap=700 overwrite=true ignorebadquality=t int=t


#Rywal STAR PE mapping
STAR \
--runMode alignReads \
--runThreadN 32 \
--genomeDir ../input/Rywal_star-index \
--readFilesIn \
../input/Rywal_cleaned_Illumina_PE_R1.fastq \
../input/Rywal_cleaned_Illumina_PE_R2.fastq \
--outFileNamePrefix ../output/Rywal_mapToEvigene_STAR_PE_ \
--outSAMtype BAM SortedByCoordinate


mkdir ../output/output_STAR_bams
mv ../output/*.bam ../output/output_STAR_bams/

#index bam file
samtools index ../output/output_STAR_bams/Desiree_mapToEvigene_STAR_SE_Aligned.sortedByCoord.out.bam
samtools index ../output/output_STAR_bams/Desiree_mapToEvigene_STAR_PE_Aligned.sortedByCoord.out.bam
#index bam file
samtools index ../output/output_STAR_bams/PW363_mapToEvigene_STAR_PE_Aligned.sortedByCoord.out.bam
#index bam file
samtools index ../output/output_STAR_bams/Rywal_mapToEvigene_STAR_SE_Aligned.sortedByCoord.out.bam
samtools index ../output/output_STAR_bams/Rywal_mapToEvigene_STAR_PE_Aligned.sortedByCoord.out.bam

mkdir ../output/output_STAR_logs-n-SJ
mv ../output/*.out* ../output/output_STAR_logs-n-SJ/
tar -zcvf ../output/output_STAR_logs-n-SJ.tar.gz ../output/output_STAR_logs-n-SJ/
rm -rf ../output/output_STAR_logs-n-SJ

rm ../input/*Desiree*
rm ../input/*PW363*
rm ../input/*Rywal*

tar -cvf ../output/output_STAR_bams.tar ../output/output_STAR_bams
rm -rf ../output/output_STAR_bams