##mapping reads back to rnaspades assembly using STAR to check the percentage of reads that map
#run on bufo

cd /DATA/markop/Pcitri_rnaspades
mkdir star_index

#the ordinary filtered (transcripts.fasta) file was used as a reference, although probably the hard_filtered transcripts would also be fine for looking for the new putative sex pheromone synthase enzymes
./STAR/bin/Linux_x86_64/STARlong --runThreadN 32 --runMode genomeGenerate --genomeDir ./star_index --genomeFastaFiles ./output/transcripts.fasta --limitGenomeGenerateRAM=220000000000


mkdir STAR_mapToAssembly

#this command doesn't work because you cannot have paired and single end reads in same mapping!!!
#also with multiple PE samples separated with comma I get a Segmentation fault error :( will do each sample separately
# ./STAR/bin/Linux_x86_64/STAR \
# --runMode alignReads \
# --runThreadN 32 \
# --genomeDir ./star_index \
# --readFilesCommand gzip -c \
# --readFilesIn \
# /FITO_ws/markop/pcitri_trimmed/PRO1976_S1_VF_2_GGAAGAGA-CGAGAGAA_L007_R1_trimmed_paired.R1.fastq.gz \
# /FITO_ws/markop/pcitri_trimmed/PRO1976_S1_VF_2_GGAAGAGA-CGAGAGAA_L007_R1_trimmed_paired.R2.fastq.gz,\
# /FITO_ws/markop/pcitri_trimmed/PRO1976_S1_VF_2_GGAAGAGA-CGAGAGAA_L007_R1_trimmed_orphans.R1.fastq.gz,\
# /FITO_ws/markop/pcitri_trimmed/PRO1976_S2_VF_3_TCGGATTC-CGCAACTA_L007_R1_trimmed_paired.R1.fastq.gz \
# /FITO_ws/markop/pcitri_trimmed/PRO1976_S2_VF_3_TCGGATTC-CGCAACTA_L007_R1_trimmed_paired.R2.fastq.gz,\
# /FITO_ws/markop/pcitri_trimmed/PRO1976_S2_VF_3_TCGGATTC-CGCAACTA_L007_R1_trimmed_orphans.R1.fastq.gz,\
# /FITO_ws/markop/pcitri_trimmed/PRO1976_S3_VF_5_CTGTACCA-CACAGACT_L007_R1_trimmed_paired.R1.fastq.gz \
# /FITO_ws/markop/pcitri_trimmed/PRO1976_S3_VF_5_CTGTACCA-CACAGACT_L007_R1_trimmed_paired.R2.fastq.gz,\
# /FITO_ws/markop/pcitri_trimmed/PRO1976_S3_VF_5_CTGTACCA-CACAGACT_L007_R1_trimmed_orphans.R1.fastq.gz,\
# /FITO_ws/markop/pcitri_trimmed/PRO1976_S4_VF_6_GAGAGTAC-TGGAAGCA_L007_R1_trimmed_paired.R1.fastq.gz \
# /FITO_ws/markop/pcitri_trimmed/PRO1976_S4_VF_6_GAGAGTAC-TGGAAGCA_L007_R1_trimmed_paired.R2.fastq.gz,\
# /FITO_ws/markop/pcitri_trimmed/PRO1976_S4_VF_6_GAGAGTAC-TGGAAGCA_L007_R1_trimmed_orphans.R1.fastq.gz \
# --outFileNamePrefix ./STAR_mapToAssembly/Pcitri_mapToAssembly_STAR \
# --outSAMtype BAM SortedByCoordinate \
# --outReadsUnmapped Fastx

# default --outFilterMultimapNmax 20

##mapping only paired reads

#ulimit default 1024
ulimit -n 10000

#S1
./STAR/bin/Linux_x86_64/STAR \
--runMode alignReads \
--runThreadN 32 \
--genomeDir ./star_index \
--readFilesIn \
./input/PRO1976_S1_VF_2_GGAAGAGA-CGAGAGAA_L007_R1_trimmed_paired.R1.fastq \
./input/PRO1976_S1_VF_2_GGAAGAGA-CGAGAGAA_L007_R1_trimmed_paired.R2.fastq \
--outFileNamePrefix ./STAR_mapToAssembly/Pcitri_mapToAssembly_STAR_S1_ \
--outSAMtype BAM SortedByCoordinate \
--outReadsUnmapped Fastx

#S2
./STAR/bin/Linux_x86_64/STAR \
--runMode alignReads \
--runThreadN 32 \
--genomeDir ./star_index \
--readFilesIn \
./input/PRO1976_S2_VF_3_TCGGATTC-CGCAACTA_L007_R1_trimmed_paired.R1.fastq \
./input/PRO1976_S2_VF_3_TCGGATTC-CGCAACTA_L007_R1_trimmed_paired.R2.fastq \
--outFileNamePrefix ./STAR_mapToAssembly/Pcitri_mapToAssembly_STAR_S2_ \
--outSAMtype BAM SortedByCoordinate \
--outReadsUnmapped Fastx

#S3
./STAR/bin/Linux_x86_64/STAR \
--runMode alignReads \
--runThreadN 32 \
--genomeDir ./star_index \
--readFilesIn \
./input/PRO1976_S3_VF_5_CTGTACCA-CACAGACT_L007_R1_trimmed_paired.R1.fastq \
./input/PRO1976_S3_VF_5_CTGTACCA-CACAGACT_L007_R1_trimmed_paired.R2.fastq \
--outFileNamePrefix ./STAR_mapToAssembly/Pcitri_mapToAssembly_STAR_S3_ \
--outSAMtype BAM SortedByCoordinate \
--outReadsUnmapped Fastx

#S4
./STAR/bin/Linux_x86_64/STAR \
--runMode alignReads \
--runThreadN 32 \
--genomeDir ./star_index \
--readFilesIn \
./input/PRO1976_S4_VF_6_GAGAGTAC-TGGAAGCA_L007_R1_trimmed_paired.R1.fastq \
./input/PRO1976_S4_VF_6_GAGAGTAC-TGGAAGCA_L007_R1_trimmed_paired.R2.fastq \
--outFileNamePrefix ./STAR_mapToAssembly/Pcitri_mapToAssembly_STAR_S4_ \
--outSAMtype BAM SortedByCoordinate \
--outReadsUnmapped Fastx


#index bam files
/DATA/majak/samtools-1.6/samtools index ./STAR_mapToAssembly/Pcitri_mapToAssembly_STAR_S1_Aligned.sortedByCoord.out.bam
/DATA/majak/samtools-1.6/samtools index ./STAR_mapToAssembly/Pcitri_mapToAssembly_STAR_S2_Aligned.sortedByCoord.out.bam
/DATA/majak/samtools-1.6/samtools index ./STAR_mapToAssembly/Pcitri_mapToAssembly_STAR_S3_Aligned.sortedByCoord.out.bam
/DATA/majak/samtools-1.6/samtools index ./STAR_mapToAssembly/Pcitri_mapToAssembly_STAR_S4_Aligned.sortedByCoord.out.bam